Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 21:34:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/10_2023/7e1y_30946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/10_2023/7e1y_30946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/10_2023/7e1y_30946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/10_2023/7e1y_30946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/10_2023/7e1y_30946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/10_2023/7e1y_30946.pdb" } resolution = 2.9 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= 0.005 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 23248 2.51 5 N 5959 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C ARG 566": "NH1" <-> "NH2" Residue "C GLU 584": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E GLU 509": "OE1" <-> "OE2" Residue "E GLU 549": "OE1" <-> "OE2" Residue "E ARG 566": "NH1" <-> "NH2" Residue "E GLU 584": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 212": "NH1" <-> "NH2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F GLU 480": "OE1" <-> "OE2" Residue "F GLU 492": "OE1" <-> "OE2" Residue "F ARG 566": "NH1" <-> "NH2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "G ARG 212": "NH1" <-> "NH2" Residue "G GLU 330": "OE1" <-> "OE2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "G TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 509": "OE1" <-> "OE2" Residue "G GLU 524": "OE1" <-> "OE2" Residue "G ARG 566": "NH1" <-> "NH2" Residue "G GLU 584": "OE1" <-> "OE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 212": "NH1" <-> "NH2" Residue "H GLU 257": "OE1" <-> "OE2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "H GLU 322": "OE1" <-> "OE2" Residue "H GLU 549": "OE1" <-> "OE2" Residue "H GLU 562": "OE1" <-> "OE2" Residue "H ARG 566": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 35743 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "B" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "C" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "D" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "E" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "F" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "G" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "H" Number of atoms: 4467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4580 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AHIS A 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 140 " occ=0.50 residue: pdb=" N AHIS B 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 140 " occ=0.50 residue: pdb=" N AHIS C 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 140 " occ=0.50 residue: pdb=" N AHIS D 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 140 " occ=0.50 residue: pdb=" N AHIS E 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 140 " occ=0.50 residue: pdb=" N AHIS F 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 140 " occ=0.50 residue: pdb=" N AHIS G 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS G 140 " occ=0.50 Time building chain proxies: 30.69, per 1000 atoms: 0.86 Number of scatterers: 35743 At special positions: 0 Unit cell: (189.618, 140.946, 193.674, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 6440 8.00 N 5959 7.00 C 23248 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: 11.77 Conformation dependent library (CDL) restraints added in 8.8 seconds 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8192 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 49 sheets defined 42.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.620A pdb=" N ILE A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 147 " --> pdb=" O TRP A 143 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.543A pdb=" N ASN A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.664A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 3.913A pdb=" N GLU A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.774A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 356 through 377 removed outlier: 3.639A pdb=" N TRP A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 419 removed outlier: 3.686A pdb=" N THR A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 461 through 483 removed outlier: 3.521A pdb=" N LYS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.641A pdb=" N ALA A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.697A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 523 " --> pdb=" O TRP A 519 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.674A pdb=" N ILE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 147 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.610A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.168A pdb=" N GLN B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 227 removed outlier: 3.707A pdb=" N THR B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 271 removed outlier: 3.821A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 341 through 351 removed outlier: 3.812A pdb=" N LEU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 377 removed outlier: 3.784A pdb=" N TRP B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 398 through 419 removed outlier: 3.842A pdb=" N THR B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 416 " --> pdb=" O TYR B 412 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 483 Processing helix chain 'B' and resid 487 through 501 removed outlier: 3.757A pdb=" N HIS B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.754A pdb=" N TRP B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.598A pdb=" N ILE B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.774A pdb=" N ASN C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.818A pdb=" N ALA C 191 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.547A pdb=" N ASN C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 270 removed outlier: 3.770A pdb=" N VAL C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 289 through 297 removed outlier: 4.304A pdb=" N ILE C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 4.040A pdb=" N LEU C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 377 removed outlier: 3.969A pdb=" N TRP C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP C 375 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 398 through 419 removed outlier: 3.786A pdb=" N THR C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 462 through 483 Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.571A pdb=" N ALA C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.877A pdb=" N TRP C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 532 removed outlier: 3.639A pdb=" N ILE C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 518 " --> pdb=" O LYS C 514 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 522 " --> pdb=" O THR C 518 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.521A pdb=" N TYR D 147 " --> pdb=" O TRP D 143 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.673A pdb=" N ASN D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.559A pdb=" N ALA D 191 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.522A pdb=" N GLU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 252 through 271 removed outlier: 3.748A pdb=" N GLU D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.491A pdb=" N ILE D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 4.140A pdb=" N LEU D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 377 removed outlier: 4.035A pdb=" N TRP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 419 removed outlier: 3.880A pdb=" N THR D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 403 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 404 " --> pdb=" O PRO D 400 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 415 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 416 " --> pdb=" O TYR D 412 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN D 419 " --> pdb=" O THR D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 462 through 483 removed outlier: 3.602A pdb=" N LYS D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 501 removed outlier: 3.747A pdb=" N HIS D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 501 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 507 removed outlier: 3.772A pdb=" N TRP D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 3.538A pdb=" N ILE D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.524A pdb=" N SER E 165 " --> pdb=" O TYR E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.746A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 removed outlier: 3.527A pdb=" N GLU E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 248 Processing helix chain 'E' and resid 251 through 270 removed outlier: 3.875A pdb=" N VAL E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 289 through 297 removed outlier: 4.368A pdb=" N ILE E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 removed outlier: 3.958A pdb=" N LEU E 348 " --> pdb=" O LEU E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 377 removed outlier: 3.886A pdb=" N TRP E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TRP E 375 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP E 377 " --> pdb=" O GLU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 398 through 419 removed outlier: 3.535A pdb=" N THR E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 403 " --> pdb=" O PRO E 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 404 " --> pdb=" O PRO E 400 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 416 " --> pdb=" O TYR E 412 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN E 419 " --> pdb=" O THR E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 434 Processing helix chain 'E' and resid 461 through 483 removed outlier: 3.533A pdb=" N TYR E 465 " --> pdb=" O GLN E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 501 removed outlier: 3.972A pdb=" N ALA E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS E 499 " --> pdb=" O TRP E 495 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 500 " --> pdb=" O ALA E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 3.681A pdb=" N TRP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 532 removed outlier: 3.505A pdb=" N ILE E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 518 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG E 530 " --> pdb=" O ILE E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.573A pdb=" N LEU F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 208 through 227 removed outlier: 3.511A pdb=" N LEU F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 248 Processing helix chain 'F' and resid 252 through 270 removed outlier: 3.752A pdb=" N GLU F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 289 through 297 removed outlier: 4.304A pdb=" N ILE F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 350 removed outlier: 3.957A pdb=" N LEU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 377 removed outlier: 3.907A pdb=" N TRP F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 398 through 419 removed outlier: 3.849A pdb=" N THR F 402 " --> pdb=" O ASN F 398 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 404 " --> pdb=" O PRO F 400 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU F 416 " --> pdb=" O TYR F 412 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 434 Processing helix chain 'F' and resid 459 through 461 No H-bonds generated for 'chain 'F' and resid 459 through 461' Processing helix chain 'F' and resid 462 through 483 Processing helix chain 'F' and resid 487 through 501 removed outlier: 3.512A pdb=" N TRP F 498 " --> pdb=" O ARG F 494 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS F 499 " --> pdb=" O TRP F 495 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 500 " --> pdb=" O ALA F 496 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 507 removed outlier: 3.832A pdb=" N TRP F 506 " --> pdb=" O ASP F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 511 removed outlier: 3.711A pdb=" N TRP F 511 " --> pdb=" O ALA F 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 508 through 511' Processing helix chain 'F' and resid 512 through 532 removed outlier: 3.588A pdb=" N ILE F 516 " --> pdb=" O LEU F 512 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE F 526 " --> pdb=" O VAL F 522 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 530 " --> pdb=" O ILE F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.727A pdb=" N ILE G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 147 " --> pdb=" O TRP G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 142 through 147' Processing helix chain 'G' and resid 159 through 171 removed outlier: 3.600A pdb=" N LEU G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 208 through 227 removed outlier: 4.060A pdb=" N THR G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 248 Processing helix chain 'G' and resid 251 through 271 removed outlier: 3.601A pdb=" N VAL G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 289 through 297 removed outlier: 4.176A pdb=" N ILE G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 350 removed outlier: 3.523A pdb=" N LEU G 348 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 377 removed outlier: 3.608A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP G 361 " --> pdb=" O GLU G 357 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP G 375 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP G 377 " --> pdb=" O GLU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 398 through 419 removed outlier: 3.679A pdb=" N THR G 402 " --> pdb=" O ASN G 398 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 403 " --> pdb=" O PRO G 399 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR G 404 " --> pdb=" O PRO G 400 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR G 415 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN G 419 " --> pdb=" O THR G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 461 through 483 removed outlier: 3.575A pdb=" N TYR G 465 " --> pdb=" O GLN G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 501 removed outlier: 3.689A pdb=" N HIS G 499 " --> pdb=" O TRP G 495 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 501 " --> pdb=" O LEU G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 507 removed outlier: 3.760A pdb=" N TRP G 506 " --> pdb=" O ASP G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 532 removed outlier: 3.583A pdb=" N ILE G 516 " --> pdb=" O LEU G 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 522 " --> pdb=" O THR G 518 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 527 " --> pdb=" O ALA G 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG G 530 " --> pdb=" O ILE G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.075A pdb=" N ARG H 116 " --> pdb=" O PRO H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.509A pdb=" N LEU H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.623A pdb=" N ALA H 191 " --> pdb=" O GLN H 187 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU H 193 " --> pdb=" O GLN H 189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 227 removed outlier: 3.626A pdb=" N GLU H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 248 Processing helix chain 'H' and resid 252 through 270 removed outlier: 3.621A pdb=" N GLU H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG H 260 " --> pdb=" O GLU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 285 Processing helix chain 'H' and resid 289 through 297 removed outlier: 4.283A pdb=" N ILE H 293 " --> pdb=" O LYS H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 351 removed outlier: 4.098A pdb=" N LEU H 348 " --> pdb=" O LEU H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 377 removed outlier: 3.572A pdb=" N ALA H 360 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP H 377 " --> pdb=" O GLU H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 419 removed outlier: 3.784A pdb=" N THR H 402 " --> pdb=" O ASN H 398 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 403 " --> pdb=" O PRO H 399 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR H 404 " --> pdb=" O PRO H 400 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN H 419 " --> pdb=" O THR H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 434 Processing helix chain 'H' and resid 459 through 461 No H-bonds generated for 'chain 'H' and resid 459 through 461' Processing helix chain 'H' and resid 462 through 483 Processing helix chain 'H' and resid 487 through 501 removed outlier: 3.569A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS H 499 " --> pdb=" O TRP H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 507 removed outlier: 3.752A pdb=" N TRP H 506 " --> pdb=" O ASP H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 532 removed outlier: 3.505A pdb=" N ILE H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 522 " --> pdb=" O THR H 518 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 523 " --> pdb=" O TRP H 519 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG H 530 " --> pdb=" O ILE H 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 305 removed outlier: 5.500A pdb=" N ASN A 442 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 439 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU A 314 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 538 " --> pdb=" O THR C 556 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG C 558 " --> pdb=" O ILE C 536 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE C 536 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 305 removed outlier: 5.500A pdb=" N ASN A 442 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 439 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU A 314 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 541 removed outlier: 5.777A pdb=" N ILE A 536 " --> pdb=" O ARG A 558 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 558 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 538 " --> pdb=" O THR A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.665A pdb=" N GLU A 584 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 616 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 230 through 232 removed outlier: 7.799A pdb=" N THR B 177 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE B 123 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 179 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 125 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 232 removed outlier: 7.799A pdb=" N THR B 177 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE B 123 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 179 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 125 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET B 119 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 305 removed outlier: 6.493A pdb=" N THR B 302 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG B 340 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 304 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN B 442 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 439 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 314 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 592 " --> pdb=" O ASN E 559 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP E 538 " --> pdb=" O THR E 556 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 558 " --> pdb=" O ILE E 536 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE E 536 " --> pdb=" O ARG E 558 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 305 removed outlier: 6.493A pdb=" N THR B 302 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG B 340 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 304 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN B 442 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 439 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 314 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 534 through 541 removed outlier: 5.762A pdb=" N ILE B 536 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 558 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 538 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 545 through 546 removed outlier: 6.655A pdb=" N PHE B 545 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 614 " --> pdb=" O ILE B 621 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 623 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 612 " --> pdb=" O SER B 623 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 625 " --> pdb=" O MET B 610 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N MET B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP B 627 " --> pdb=" O HIS B 608 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS B 608 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN B 629 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B 606 " --> pdb=" O ASN B 629 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 605 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP C 622 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LYS B 607 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS C 624 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS B 609 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ILE C 626 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL B 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N ILE C 628 " --> pdb=" O VAL B 611 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N SER B 613 " --> pdb=" O ILE C 628 " (cutoff:3.500A) removed outlier: 14.505A pdb=" N VAL C 630 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 13.462A pdb=" N ILE B 615 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 545 " --> pdb=" O LYS C 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 545 through 546 removed outlier: 6.655A pdb=" N PHE B 545 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS C 607 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 622 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LYS C 609 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS B 624 " --> pdb=" O LYS C 609 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL C 611 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 12.288A pdb=" N ILE B 626 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N SER C 613 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 14.172A pdb=" N ILE B 628 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 13.507A pdb=" N ILE C 615 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 15.368A pdb=" N VAL B 630 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 584 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 545 through 546 removed outlier: 6.655A pdb=" N PHE B 545 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS C 607 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 622 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LYS C 609 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS B 624 " --> pdb=" O LYS C 609 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL C 611 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 12.288A pdb=" N ILE B 626 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N SER C 613 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 14.172A pdb=" N ILE B 628 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 13.507A pdb=" N ILE C 615 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 15.368A pdb=" N VAL B 630 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP C 622 " --> pdb=" O ALA C 614 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER C 616 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 605 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP C 622 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LYS B 607 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS C 624 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS B 609 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ILE C 626 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL B 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N ILE C 628 " --> pdb=" O VAL B 611 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N SER B 613 " --> pdb=" O ILE C 628 " (cutoff:3.500A) removed outlier: 14.505A pdb=" N VAL C 630 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 13.462A pdb=" N ILE B 615 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 584 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 232 removed outlier: 7.741A pdb=" N THR C 177 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE C 123 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN C 179 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP C 125 " --> pdb=" O ASN C 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 230 through 232 removed outlier: 7.741A pdb=" N THR C 177 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE C 123 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN C 179 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP C 125 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET C 119 " --> pdb=" O LYS C 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 234 through 235 removed outlier: 7.070A pdb=" N THR C 234 " --> pdb=" O TRP C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 305 removed outlier: 5.593A pdb=" N ASN C 442 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU C 314 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 230 through 232 Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 232 removed outlier: 6.879A pdb=" N MET D 119 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.731A pdb=" N THR D 234 " --> pdb=" O TRP D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 301 through 305 removed outlier: 6.311A pdb=" N THR D 302 " --> pdb=" O PHE D 338 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG D 340 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 304 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET D 325 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN D 442 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE D 327 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 439 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU D 314 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 595 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP H 538 " --> pdb=" O THR H 556 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG H 558 " --> pdb=" O ILE H 536 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE H 536 " --> pdb=" O ARG H 558 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 301 through 305 removed outlier: 6.311A pdb=" N THR D 302 " --> pdb=" O PHE D 338 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG D 340 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 304 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET D 325 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN D 442 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE D 327 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 439 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU D 314 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 595 " --> pdb=" O GLY D 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 534 through 541 removed outlier: 5.731A pdb=" N ILE D 536 " --> pdb=" O ARG D 558 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG D 558 " --> pdb=" O ILE D 536 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 538 " --> pdb=" O THR D 556 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 584 through 585 removed outlier: 3.852A pdb=" N GLU D 584 " --> pdb=" O PHE D 569 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY D 606 " --> pdb=" O ASN D 629 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN D 629 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS D 608 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP D 627 " --> pdb=" O HIS D 608 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET D 610 " --> pdb=" O ILE D 625 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE D 625 " --> pdb=" O MET D 610 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 612 " --> pdb=" O SER D 623 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER D 623 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA D 614 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 230 through 232 removed outlier: 3.612A pdb=" N ASP E 231 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR E 177 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 123 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN E 179 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP E 125 " --> pdb=" O ASN E 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 230 through 232 removed outlier: 3.612A pdb=" N ASP E 231 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR E 177 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 123 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN E 179 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP E 125 " --> pdb=" O ASN E 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 234 through 235 removed outlier: 6.905A pdb=" N THR E 234 " --> pdb=" O TRP E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 301 through 304 Processing sheet with id=AD3, first strand: chain 'E' and resid 314 through 315 removed outlier: 6.529A pdb=" N GLU E 314 " --> pdb=" O THR E 441 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 545 through 546 removed outlier: 6.787A pdb=" N PHE E 545 " --> pdb=" O LYS E 631 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA E 614 " --> pdb=" O ILE E 621 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER E 623 " --> pdb=" O VAL E 612 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E 612 " --> pdb=" O SER E 623 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE E 625 " --> pdb=" O MET E 610 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N MET E 610 " --> pdb=" O ILE E 625 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP E 627 " --> pdb=" O HIS E 608 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS E 608 " --> pdb=" O ASP E 627 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN E 629 " --> pdb=" O GLY E 606 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY E 606 " --> pdb=" O ASN E 629 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU E 584 " --> pdb=" O PHE E 569 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 230 through 232 removed outlier: 3.719A pdb=" N ASP F 231 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 230 through 232 removed outlier: 3.719A pdb=" N ASP F 231 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET F 119 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 234 through 235 removed outlier: 6.797A pdb=" N THR F 234 " --> pdb=" O TRP F 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 301 through 305 removed outlier: 6.385A pdb=" N THR F 302 " --> pdb=" O PHE F 338 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG F 340 " --> pdb=" O THR F 302 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU F 304 " --> pdb=" O ARG F 340 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N MET F 325 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN F 442 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ILE F 327 " --> pdb=" O ASN F 442 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU F 314 " --> pdb=" O THR F 441 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 534 through 541 removed outlier: 5.798A pdb=" N ILE F 536 " --> pdb=" O ARG F 558 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG F 558 " --> pdb=" O ILE F 536 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP F 538 " --> pdb=" O THR F 556 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN G 316 " --> pdb=" O LEU G 440 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU G 440 " --> pdb=" O ASN G 316 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN G 442 " --> pdb=" O ILE G 327 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR G 302 " --> pdb=" O PHE G 338 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG G 340 " --> pdb=" O THR G 302 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU G 304 " --> pdb=" O ARG G 340 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 545 through 546 removed outlier: 6.934A pdb=" N PHE F 545 " --> pdb=" O LYS F 631 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 584 through 585 removed outlier: 3.893A pdb=" N GLU F 584 " --> pdb=" O PHE F 569 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER F 616 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE F 620 " --> pdb=" O SER F 616 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 577 through 578 Processing sheet with id=AE4, first strand: chain 'G' and resid 230 through 232 removed outlier: 8.014A pdb=" N THR G 177 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE G 123 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN G 179 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP G 125 " --> pdb=" O ASN G 179 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 230 through 232 removed outlier: 8.014A pdb=" N THR G 177 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE G 123 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN G 179 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP G 125 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET G 119 " --> pdb=" O LYS G 423 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 234 through 235 removed outlier: 6.893A pdb=" N THR G 234 " --> pdb=" O TRP G 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 534 through 538 removed outlier: 6.772A pdb=" N THR G 556 " --> pdb=" O ILE G 537 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 584 through 585 removed outlier: 3.942A pdb=" N GLU G 584 " --> pdb=" O PHE G 569 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER G 616 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE G 620 " --> pdb=" O SER G 616 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS H 607 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP G 622 " --> pdb=" O LYS H 607 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LYS H 609 " --> pdb=" O ASP G 622 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LYS G 624 " --> pdb=" O LYS H 609 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL H 611 " --> pdb=" O LYS G 624 " (cutoff:3.500A) removed outlier: 12.555A pdb=" N ILE G 626 " --> pdb=" O VAL H 611 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N SER H 613 " --> pdb=" O ILE G 626 " (cutoff:3.500A) removed outlier: 14.409A pdb=" N ILE G 628 " --> pdb=" O SER H 613 " (cutoff:3.500A) removed outlier: 13.652A pdb=" N ILE H 615 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 15.512A pdb=" N VAL G 630 " --> pdb=" O ILE H 615 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER H 616 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE H 545 " --> pdb=" O LYS H 631 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 584 through 585 removed outlier: 3.942A pdb=" N GLU G 584 " --> pdb=" O PHE G 569 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER G 616 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE G 620 " --> pdb=" O SER G 616 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS H 607 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP G 622 " --> pdb=" O LYS H 607 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LYS H 609 " --> pdb=" O ASP G 622 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LYS G 624 " --> pdb=" O LYS H 609 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL H 611 " --> pdb=" O LYS G 624 " (cutoff:3.500A) removed outlier: 12.555A pdb=" N ILE G 626 " --> pdb=" O VAL H 611 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N SER H 613 " --> pdb=" O ILE G 626 " (cutoff:3.500A) removed outlier: 14.409A pdb=" N ILE G 628 " --> pdb=" O SER H 613 " (cutoff:3.500A) removed outlier: 13.652A pdb=" N ILE H 615 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 15.512A pdb=" N VAL G 630 " --> pdb=" O ILE H 615 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 584 " --> pdb=" O PHE H 569 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 230 through 232 removed outlier: 3.633A pdb=" N ASP H 231 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP H 125 " --> pdb=" O THR H 177 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 230 through 232 removed outlier: 3.633A pdb=" N ASP H 231 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP H 125 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET H 119 " --> pdb=" O LYS H 423 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 234 through 235 removed outlier: 6.771A pdb=" N THR H 234 " --> pdb=" O TRP H 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 301 through 305 removed outlier: 6.140A pdb=" N MET H 325 " --> pdb=" O LEU H 440 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN H 442 " --> pdb=" O MET H 325 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 327 " --> pdb=" O ASN H 442 " (cutoff:3.500A) 1535 hydrogen bonds defined for protein. 4410 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: 13.27 Time building geometry restraints manager: 12.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 10652 1.33 - 1.45: 6270 1.45 - 1.57: 19717 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 36823 Sorted by residual: bond pdb=" N VAL C 567 " pdb=" CA VAL C 567 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" N ILE C 565 " pdb=" CA ILE C 565 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" N SER E 150 " pdb=" CA SER E 150 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.22e-02 6.72e+03 1.01e+01 bond pdb=" N GLU A 357 " pdb=" CA GLU A 357 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.89e+00 bond pdb=" N VAL C 555 " pdb=" CA VAL C 555 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.14e+00 ... (remaining 36818 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.93: 703 104.93 - 112.26: 17815 112.26 - 119.59: 12779 119.59 - 126.91: 18074 126.91 - 134.24: 691 Bond angle restraints: 50062 Sorted by residual: angle pdb=" N THR H 329 " pdb=" CA THR H 329 " pdb=" C THR H 329 " ideal model delta sigma weight residual 111.07 119.01 -7.94 1.07e+00 8.73e-01 5.51e+01 angle pdb=" N ARG B 566 " pdb=" CA ARG B 566 " pdb=" C ARG B 566 " ideal model delta sigma weight residual 107.69 121.79 -14.10 2.01e+00 2.48e-01 4.92e+01 angle pdb=" C SER H 319 " pdb=" CA SER H 319 " pdb=" CB SER H 319 " ideal model delta sigma weight residual 110.16 101.84 8.32 1.83e+00 2.99e-01 2.07e+01 angle pdb=" N TYR E 147 " pdb=" CA TYR E 147 " pdb=" C TYR E 147 " ideal model delta sigma weight residual 111.28 106.39 4.89 1.09e+00 8.42e-01 2.02e+01 angle pdb=" N GLN H 320 " pdb=" CA GLN H 320 " pdb=" C GLN H 320 " ideal model delta sigma weight residual 113.15 117.87 -4.72 1.19e+00 7.06e-01 1.57e+01 ... (remaining 50057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 19796 17.77 - 35.53: 1520 35.53 - 53.30: 233 53.30 - 71.06: 45 71.06 - 88.83: 22 Dihedral angle restraints: 21616 sinusoidal: 8864 harmonic: 12752 Sorted by residual: dihedral pdb=" CA HIS H 128 " pdb=" C HIS H 128 " pdb=" N GLN H 129 " pdb=" CA GLN H 129 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA HIS F 128 " pdb=" C HIS F 128 " pdb=" N GLN F 129 " pdb=" CA GLN F 129 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER G 543 " pdb=" C SER G 543 " pdb=" N GLU G 544 " pdb=" CA GLU G 544 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 21613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4606 0.074 - 0.148: 666 0.148 - 0.222: 30 0.222 - 0.296: 1 0.296 - 0.370: 1 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA ARG C 566 " pdb=" N ARG C 566 " pdb=" C ARG C 566 " pdb=" CB ARG C 566 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA THR H 329 " pdb=" N THR H 329 " pdb=" C THR H 329 " pdb=" CB THR H 329 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA LYS C 475 " pdb=" N LYS C 475 " pdb=" C LYS C 475 " pdb=" CB LYS C 475 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 5301 not shown) Planarity restraints: 6335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 448 " 0.041 2.00e-02 2.50e+03 3.61e-02 3.26e+01 pdb=" CG TRP B 448 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP B 448 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 448 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 448 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 448 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 448 " -0.037 2.00e-02 2.50e+03 3.44e-02 2.96e+01 pdb=" CG TRP A 448 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP A 448 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 448 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 448 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 448 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 448 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 448 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 448 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 448 " -0.037 2.00e-02 2.50e+03 3.34e-02 2.79e+01 pdb=" CG TRP C 448 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP C 448 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 448 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 448 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 448 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 448 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 448 " -0.001 2.00e-02 2.50e+03 ... (remaining 6332 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2582 2.74 - 3.28: 35782 3.28 - 3.82: 59941 3.82 - 4.36: 76441 4.36 - 4.90: 129674 Nonbonded interactions: 304420 Sorted by model distance: nonbonded pdb=" OG1 THR A 574 " pdb=" OG SER E 613 " model vdw 2.195 2.440 nonbonded pdb=" OG SER D 578 " pdb=" OD1 ASN D 581 " model vdw 2.218 2.440 nonbonded pdb=" NZ LYS C 607 " pdb=" OD1 ASP C 627 " model vdw 2.232 2.520 nonbonded pdb=" OG SER G 613 " pdb=" OG1 THR H 574 " model vdw 2.239 2.440 nonbonded pdb=" NE2 HIS A 359 " pdb=" OD1 ASN A 363 " model vdw 2.249 2.520 ... (remaining 304415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'B' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'C' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'D' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'E' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'F' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'G' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'H' and (resid 103 through 139 or resid 141 through 640)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.470 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 102.330 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.200 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 36823 Z= 0.276 Angle : 0.758 14.103 50062 Z= 0.470 Chirality : 0.050 0.370 5304 Planarity : 0.005 0.093 6335 Dihedral : 13.003 88.831 13424 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.12), residues: 4311 helix: -1.20 (0.12), residues: 1624 sheet: -1.14 (0.18), residues: 880 loop : -1.72 (0.13), residues: 1807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 874 time to evaluate : 4.045 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 874 average time/residue: 1.7038 time to fit residues: 1747.6734 Evaluate side-chains 528 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 527 time to evaluate : 4.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 5.7936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 385 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 277 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 532 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 273 ASN B 359 HIS ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** C 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 353 ASN D 398 ASN D 461 GLN E 379 ASN F 129 GLN ** F 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 363 ASN G 171 HIS ** G 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN H 127 HIS H 129 GLN H 189 GLN H 353 ASN H 608 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36823 Z= 0.288 Angle : 0.658 8.435 50062 Z= 0.353 Chirality : 0.050 0.227 5304 Planarity : 0.006 0.069 6335 Dihedral : 4.854 20.197 4744 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.60 % Allowed : 11.75 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.49 (0.12), residues: 4311 helix: -0.37 (0.12), residues: 1656 sheet: -0.87 (0.18), residues: 904 loop : -1.53 (0.13), residues: 1751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 574 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 27 residues processed: 624 average time/residue: 1.6550 time to fit residues: 1222.6273 Evaluate side-chains 517 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 490 time to evaluate : 4.234 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 11 average time/residue: 0.7401 time to fit residues: 17.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 320 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 416 optimal weight: 2.9990 chunk 343 optimal weight: 8.9990 chunk 382 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 309 optimal weight: 0.7980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 171 HIS A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN B 273 ASN B 461 GLN B 532 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN D 461 GLN E 379 ASN G 118 GLN G 189 GLN G 391 ASN ** G 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 HIS H 129 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 36823 Z= 0.462 Angle : 0.734 9.802 50062 Z= 0.390 Chirality : 0.054 0.197 5304 Planarity : 0.006 0.062 6335 Dihedral : 5.143 24.566 4744 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.99 % Allowed : 13.74 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4311 helix: -0.32 (0.12), residues: 1672 sheet: -0.37 (0.18), residues: 848 loop : -1.56 (0.13), residues: 1791 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 528 time to evaluate : 3.839 Fit side-chains revert: symmetry clash outliers start: 116 outliers final: 50 residues processed: 597 average time/residue: 1.6914 time to fit residues: 1195.9433 Evaluate side-chains 535 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 485 time to evaluate : 4.406 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 33 residues processed: 18 average time/residue: 0.8829 time to fit residues: 26.8215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 387 optimal weight: 3.9990 chunk 409 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 366 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 273 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 207 ASN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN D 461 GLN E 162 HIS E 316 ASN E 379 ASN F 219 ASN F 277 GLN G 118 GLN G 189 GLN G 391 ASN ** G 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN H 189 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36823 Z= 0.188 Angle : 0.560 8.637 50062 Z= 0.298 Chirality : 0.047 0.186 5304 Planarity : 0.005 0.056 6335 Dihedral : 4.605 20.957 4744 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.16 % Allowed : 15.46 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.12), residues: 4311 helix: 0.29 (0.13), residues: 1672 sheet: -0.54 (0.18), residues: 904 loop : -1.25 (0.14), residues: 1735 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 538 time to evaluate : 4.353 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 37 residues processed: 589 average time/residue: 1.6467 time to fit residues: 1154.8838 Evaluate side-chains 518 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 481 time to evaluate : 4.056 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 28 residues processed: 9 average time/residue: 0.8746 time to fit residues: 16.4106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 349 optimal weight: 7.9990 chunk 283 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 367 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 219 ASN C 220 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN D 560 GLN E 208 HIS ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN F 219 ASN F 275 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 GLN G 391 ASN G 419 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN H 164 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36823 Z= 0.292 Angle : 0.609 8.941 50062 Z= 0.323 Chirality : 0.049 0.183 5304 Planarity : 0.005 0.058 6335 Dihedral : 4.702 21.590 4744 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.42 % Allowed : 15.80 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.12), residues: 4311 helix: 0.31 (0.12), residues: 1688 sheet: -0.50 (0.18), residues: 904 loop : -1.31 (0.13), residues: 1719 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 494 time to evaluate : 3.609 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 46 residues processed: 550 average time/residue: 1.6505 time to fit residues: 1075.4243 Evaluate side-chains 520 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 474 time to evaluate : 3.820 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.7252 time to fit residues: 15.3481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 7.9990 chunk 369 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 410 optimal weight: 5.9990 chunk 340 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 0.3980 chunk 215 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN D 560 GLN E 208 HIS ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN F 391 ASN G 118 GLN G 189 GLN G 391 ASN H 129 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36823 Z= 0.305 Angle : 0.618 11.413 50062 Z= 0.326 Chirality : 0.049 0.182 5304 Planarity : 0.005 0.053 6335 Dihedral : 4.749 22.442 4744 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.76 % Allowed : 16.08 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.74 (0.12), residues: 4311 helix: 0.36 (0.12), residues: 1704 sheet: -0.48 (0.18), residues: 904 loop : -1.27 (0.14), residues: 1703 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 488 time to evaluate : 4.420 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 49 residues processed: 555 average time/residue: 1.6139 time to fit residues: 1065.9086 Evaluate side-chains 514 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 465 time to evaluate : 4.224 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 36 residues processed: 13 average time/residue: 0.6576 time to fit residues: 18.2553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 299 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 408 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN D 560 GLN E 208 HIS E 379 ASN F 316 ASN F 391 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 GLN G 391 ASN H 129 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36823 Z= 0.211 Angle : 0.565 11.470 50062 Z= 0.297 Chirality : 0.047 0.189 5304 Planarity : 0.005 0.059 6335 Dihedral : 4.535 20.631 4744 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.09 % Allowed : 17.16 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.51 (0.12), residues: 4311 helix: 0.55 (0.13), residues: 1712 sheet: -0.40 (0.18), residues: 904 loop : -1.12 (0.14), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 502 time to evaluate : 4.041 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 47 residues processed: 561 average time/residue: 1.5993 time to fit residues: 1071.5094 Evaluate side-chains 519 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 472 time to evaluate : 4.118 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 38 residues processed: 9 average time/residue: 0.5576 time to fit residues: 13.1543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN D 560 GLN E 208 HIS E 379 ASN F 391 ASN G 118 GLN G 189 GLN G 391 ASN H 129 GLN H 162 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36823 Z= 0.305 Angle : 0.616 11.482 50062 Z= 0.325 Chirality : 0.049 0.244 5304 Planarity : 0.005 0.062 6335 Dihedral : 4.700 21.148 4744 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.29 % Allowed : 17.35 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.59 (0.12), residues: 4311 helix: 0.46 (0.12), residues: 1712 sheet: -0.42 (0.18), residues: 904 loop : -1.16 (0.14), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 477 time to evaluate : 4.269 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 49 residues processed: 538 average time/residue: 1.6330 time to fit residues: 1046.8000 Evaluate side-chains 513 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 464 time to evaluate : 4.323 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 41 residues processed: 8 average time/residue: 0.9977 time to fit residues: 16.5555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 10.0000 chunk 391 optimal weight: 0.0970 chunk 357 optimal weight: 0.8980 chunk 380 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 299 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 344 optimal weight: 5.9990 chunk 360 optimal weight: 0.9990 chunk 379 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 560 GLN E 171 HIS E 208 HIS E 379 ASN F 391 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 ASN H 129 GLN H 162 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 535 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36823 Z= 0.169 Angle : 0.539 9.118 50062 Z= 0.285 Chirality : 0.046 0.177 5304 Planarity : 0.004 0.054 6335 Dihedral : 4.372 19.008 4744 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.49 % Allowed : 18.20 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.30 (0.13), residues: 4311 helix: 0.76 (0.13), residues: 1712 sheet: -0.35 (0.18), residues: 888 loop : -1.02 (0.14), residues: 1711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 514 time to evaluate : 4.046 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 43 residues processed: 560 average time/residue: 1.6379 time to fit residues: 1103.0892 Evaluate side-chains 521 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 478 time to evaluate : 4.180 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.4003 time to fit residues: 9.4348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.0020 chunk 402 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 422 optimal weight: 5.9990 chunk 388 optimal weight: 0.0270 chunk 336 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.5450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN D 560 GLN E 208 HIS E 379 ASN F 391 ASN G 118 GLN G 189 GLN G 239 HIS G 391 ASN H 129 GLN H 162 HIS H 219 ASN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36823 Z= 0.237 Angle : 0.586 10.566 50062 Z= 0.308 Chirality : 0.047 0.222 5304 Planarity : 0.005 0.057 6335 Dihedral : 4.482 18.196 4744 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.39 % Allowed : 18.69 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.31 (0.13), residues: 4311 helix: 0.71 (0.13), residues: 1720 sheet: -0.30 (0.18), residues: 896 loop : -1.00 (0.14), residues: 1695 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 498 time to evaluate : 4.110 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 42 residues processed: 540 average time/residue: 1.6369 time to fit residues: 1053.3316 Evaluate side-chains 519 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 477 time to evaluate : 4.435 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 36 residues processed: 6 average time/residue: 0.6289 time to fit residues: 11.1545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 0.2980 chunk 358 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 336 optimal weight: 0.1980 chunk 140 optimal weight: 0.9990 chunk 345 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 529 ASN ** C 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN E 208 HIS E 379 ASN F 391 ASN G 118 GLN G 189 GLN G 391 ASN H 129 GLN H 162 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109816 restraints weight = 166741.921| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.64 r_work: 0.2980 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36823 Z= 0.162 Angle : 0.541 10.631 50062 Z= 0.284 Chirality : 0.046 0.176 5304 Planarity : 0.004 0.052 6335 Dihedral : 4.294 18.779 4744 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.39 % Allowed : 18.84 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.16 (0.13), residues: 4311 helix: 0.86 (0.13), residues: 1720 sheet: -0.28 (0.18), residues: 888 loop : -0.91 (0.14), residues: 1703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16313.18 seconds wall clock time: 289 minutes 7.61 seconds (17347.61 seconds total)