Starting phenix.real_space_refine on Thu Feb 22 23:22:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/02_2024/7e1y_30946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/02_2024/7e1y_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_30946/02_2024/7e1y_30946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/02_2024/7e1y_30946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/02_2024/7e1y_30946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1y_30946/02_2024/7e1y_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 32.94, per 1000 atoms: 0.92 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: 14.24 Conformation dependent library (CDL) restraints added in 12.4 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: 4.39 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: 15.07 Time building geometry restraints manager: 15.37 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.540 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 116.880 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.230 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.270 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP B 448 HIS 0.018 0.002 HIS A 239 PHE 0.041 0.002 PHE H 405 TYR 0.024 0.001 TYR E 334 ARG 0.012 0.001 ARG C 260 *********************** 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 : 4.095 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8387 (p) cc_final: 0.8087 (p) REVERT: A 190 ILE cc_start: 0.8093 (pt) cc_final: 0.7644 (mt) REVERT: A 268 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8145 (ttpp) REVERT: A 351 ARG cc_start: 0.5421 (mmm160) cc_final: 0.3866 (mmp80) REVERT: A 439 ILE cc_start: 0.8317 (mm) cc_final: 0.8021 (mt) REVERT: B 226 PHE cc_start: 0.7733 (m-80) cc_final: 0.7452 (m-80) REVERT: B 351 ARG cc_start: 0.4427 (mmm160) cc_final: 0.3930 (mmm-85) REVERT: B 404 TYR cc_start: 0.7518 (t80) cc_final: 0.7182 (t80) REVERT: C 108 PHE cc_start: 0.7483 (p90) cc_final: 0.7213 (p90) REVERT: C 163 TYR cc_start: 0.7917 (t80) cc_final: 0.7682 (t80) REVERT: C 168 LEU cc_start: 0.8090 (mt) cc_final: 0.7794 (mt) REVERT: C 351 ARG cc_start: 0.5910 (mmt180) cc_final: 0.5588 (mmm160) REVERT: C 373 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 377 ASP cc_start: 0.7315 (t0) cc_final: 0.6955 (t0) REVERT: C 385 ILE cc_start: 0.8728 (mt) cc_final: 0.7826 (tt) REVERT: C 409 MET cc_start: 0.7118 (tpp) cc_final: 0.6771 (ttp) REVERT: C 623 SER cc_start: 0.7955 (p) cc_final: 0.7735 (p) REVERT: D 105 ASN cc_start: 0.6907 (t0) cc_final: 0.6697 (t0) REVERT: D 108 PHE cc_start: 0.7666 (p90) cc_final: 0.7340 (p90) REVERT: D 203 LYS cc_start: 0.7740 (ptmm) cc_final: 0.7514 (pttm) REVERT: D 288 MET cc_start: 0.8621 (mmm) cc_final: 0.8411 (mmm) REVERT: D 437 ASN cc_start: 0.7034 (p0) cc_final: 0.6648 (m110) REVERT: D 622 ASP cc_start: 0.7702 (t0) cc_final: 0.7234 (t0) REVERT: E 167 MET cc_start: 0.7182 (mmm) cc_final: 0.6720 (mmm) REVERT: E 174 PHE cc_start: 0.8113 (t80) cc_final: 0.7911 (t80) REVERT: E 199 VAL cc_start: 0.7187 (t) cc_final: 0.6909 (p) REVERT: E 319 SER cc_start: 0.7945 (p) cc_final: 0.7702 (t) REVERT: E 329 THR cc_start: 0.7388 (m) cc_final: 0.7155 (p) REVERT: E 351 ARG cc_start: 0.4757 (tpm170) cc_final: 0.2816 (ttt180) REVERT: E 363 ASN cc_start: 0.7369 (m-40) cc_final: 0.6975 (m110) REVERT: E 481 GLU cc_start: 0.7532 (tp30) cc_final: 0.7301 (tm-30) REVERT: E 588 MET cc_start: 0.7696 (ptp) cc_final: 0.7449 (ptt) REVERT: F 108 PHE cc_start: 0.7588 (p90) cc_final: 0.7388 (p90) REVERT: F 256 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7382 (tm-30) REVERT: F 275 ASN cc_start: 0.8308 (t0) cc_final: 0.8077 (t0) REVERT: F 332 LYS cc_start: 0.7953 (mmpt) cc_final: 0.7689 (mmtm) REVERT: F 351 ARG cc_start: 0.4880 (tpm170) cc_final: 0.3574 (tpt-90) REVERT: F 373 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7212 (tp30) REVERT: F 381 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7753 (ttmm) REVERT: F 510 PHE cc_start: 0.7921 (m-10) cc_final: 0.7684 (m-80) REVERT: F 585 THR cc_start: 0.7997 (t) cc_final: 0.7394 (m) REVERT: G 110 VAL cc_start: 0.7849 (t) cc_final: 0.7617 (t) REVERT: G 197 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7341 (tm-30) REVERT: G 296 ASP cc_start: 0.7869 (m-30) cc_final: 0.7627 (m-30) REVERT: G 341 ASP cc_start: 0.7928 (t70) cc_final: 0.7704 (t0) REVERT: G 391 ASN cc_start: 0.8250 (m-40) cc_final: 0.8042 (m-40) REVERT: G 411 ILE cc_start: 0.8319 (mt) cc_final: 0.8007 (mm) REVERT: G 420 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7725 (mttm) REVERT: G 596 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7255 (ptp-170) REVERT: H 118 GLN cc_start: 0.7395 (pt0) cc_final: 0.7145 (pt0) REVERT: H 120 TYR cc_start: 0.7779 (m-80) cc_final: 0.7545 (m-80) REVERT: H 163 TYR cc_start: 0.7864 (t80) cc_final: 0.7654 (t80) REVERT: H 226 PHE cc_start: 0.7867 (m-80) cc_final: 0.7626 (m-80) REVERT: H 231 ASP cc_start: 0.7269 (t0) cc_final: 0.6957 (t70) REVERT: H 328 ASP cc_start: 0.7231 (t0) cc_final: 0.6998 (t70) REVERT: H 381 LYS cc_start: 0.7663 (tppt) cc_final: 0.7253 (tppt) REVERT: H 420 LYS cc_start: 0.7578 (mmpt) cc_final: 0.7293 (mtpt) REVERT: H 481 GLU cc_start: 0.7529 (tp30) cc_final: 0.7100 (tp30) REVERT: H 566 ARG cc_start: 0.6990 (ptm-80) cc_final: 0.6717 (ptt-90) outliers start: 1 outliers final: 1 residues processed: 874 average time/residue: 1.6897 time to fit residues: 1729.4963 Evaluate side-chains 552 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 551 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ILE 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: 0.7980 chunk 178 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 385 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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 189 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN 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 353 ASN G 171 HIS G 239 HIS G 391 ASN ** G 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN H 127 HIS H 129 GLN H 189 GLN H 353 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36823 Z= 0.223 Angle : 0.618 10.998 50062 Z= 0.331 Chirality : 0.048 0.190 5304 Planarity : 0.005 0.071 6335 Dihedral : 4.713 19.403 4746 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.19 % Allowed : 11.26 % Favored : 86.55 % 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: -1.46 (0.12), residues: 4311 helix: -0.34 (0.12), residues: 1656 sheet: -0.88 (0.18), residues: 904 loop : -1.50 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 448 HIS 0.013 0.001 HIS B 239 PHE 0.026 0.002 PHE C 405 TYR 0.015 0.001 TYR F 334 ARG 0.010 0.001 ARG D 186 *********************** 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 668 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 583 time to evaluate : 3.862 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8299 (p) cc_final: 0.8045 (p) REVERT: A 190 ILE cc_start: 0.8095 (pt) cc_final: 0.7562 (mt) REVERT: A 268 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8260 (ttpt) REVERT: B 186 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7147 (ttm170) REVERT: B 226 PHE cc_start: 0.7691 (m-80) cc_final: 0.7408 (m-80) REVERT: B 343 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: B 351 ARG cc_start: 0.4795 (mmm160) cc_final: 0.4175 (mmm-85) REVERT: B 411 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7447 (pp) REVERT: B 549 GLU cc_start: 0.7357 (tt0) cc_final: 0.6869 (tm-30) REVERT: B 566 ARG cc_start: 0.6884 (ttp-110) cc_final: 0.6609 (ttm170) REVERT: C 108 PHE cc_start: 0.7456 (p90) cc_final: 0.7174 (p90) REVERT: C 167 MET cc_start: 0.7573 (mmm) cc_final: 0.7008 (mtp) REVERT: C 168 LEU cc_start: 0.7937 (mt) cc_final: 0.7630 (mt) REVERT: C 256 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: C 260 ARG cc_start: 0.7732 (ttp-110) cc_final: 0.7213 (ttm-80) REVERT: C 351 ARG cc_start: 0.6027 (mmt180) cc_final: 0.5511 (mmm-85) REVERT: C 373 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7390 (mt-10) REVERT: C 377 ASP cc_start: 0.7350 (t0) cc_final: 0.7074 (t0) REVERT: C 379 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6505 (t0) REVERT: C 385 ILE cc_start: 0.8772 (mt) cc_final: 0.7958 (tt) REVERT: D 105 ASN cc_start: 0.7209 (t0) cc_final: 0.6982 (t0) REVERT: D 108 PHE cc_start: 0.7621 (p90) cc_final: 0.7244 (p90) REVERT: D 136 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7078 (p0) REVERT: D 203 LYS cc_start: 0.7696 (ptmm) cc_final: 0.7417 (pttm) REVERT: D 216 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: D 332 LYS cc_start: 0.7990 (mttm) cc_final: 0.7680 (mmmm) REVERT: D 347 ILE cc_start: 0.8351 (tp) cc_final: 0.8078 (mt) REVERT: D 437 ASN cc_start: 0.7113 (p0) cc_final: 0.6472 (m110) REVERT: D 535 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: E 174 PHE cc_start: 0.8109 (t80) cc_final: 0.7866 (t80) REVERT: E 189 GLN cc_start: 0.7285 (tp40) cc_final: 0.6344 (tm-30) REVERT: E 199 VAL cc_start: 0.7214 (t) cc_final: 0.6910 (p) REVERT: E 283 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: E 351 ARG cc_start: 0.4792 (tpm170) cc_final: 0.2729 (ttt180) REVERT: E 363 ASN cc_start: 0.7257 (m-40) cc_final: 0.6829 (m110) REVERT: E 391 ASN cc_start: 0.7274 (m-40) cc_final: 0.6789 (t0) REVERT: E 420 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7293 (ttpt) REVERT: E 428 ARG cc_start: 0.7288 (tpp80) cc_final: 0.6788 (tpt-90) REVERT: E 481 GLU cc_start: 0.7569 (tp30) cc_final: 0.7315 (tm-30) REVERT: E 588 MET cc_start: 0.7571 (ptp) cc_final: 0.7353 (ptt) REVERT: F 173 HIS cc_start: 0.6158 (OUTLIER) cc_final: 0.5931 (m90) REVERT: F 231 ASP cc_start: 0.7841 (t70) cc_final: 0.7425 (t70) REVERT: F 332 LYS cc_start: 0.7968 (mmpt) cc_final: 0.7707 (mmtm) REVERT: F 351 ARG cc_start: 0.5043 (tpm170) cc_final: 0.3667 (tpt-90) REVERT: F 373 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6868 (tp30) REVERT: F 376 PHE cc_start: 0.7176 (m-10) cc_final: 0.6772 (m-10) REVERT: F 510 PHE cc_start: 0.7851 (m-10) cc_final: 0.7632 (m-80) REVERT: F 538 ASP cc_start: 0.7005 (p0) cc_final: 0.6804 (p0) REVERT: G 189 GLN cc_start: 0.7438 (tp40) cc_final: 0.7155 (tt0) REVERT: G 362 ARG cc_start: 0.5146 (ttm110) cc_final: 0.4031 (tmt170) REVERT: G 378 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7672 (mptt) REVERT: G 420 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7598 (mttm) REVERT: H 118 GLN cc_start: 0.7176 (pt0) cc_final: 0.6967 (pt0) REVERT: H 120 TYR cc_start: 0.7790 (m-80) cc_final: 0.7533 (m-80) REVERT: H 231 ASP cc_start: 0.7233 (t0) cc_final: 0.6826 (t70) REVERT: H 260 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7381 (ttp80) REVERT: H 295 TYR cc_start: 0.8269 (t80) cc_final: 0.7581 (t80) REVERT: H 373 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7343 (mm-30) REVERT: H 381 LYS cc_start: 0.7666 (tppt) cc_final: 0.7221 (tppt) REVERT: H 391 ASN cc_start: 0.8284 (m110) cc_final: 0.7990 (t0) REVERT: H 566 ARG cc_start: 0.6993 (ptm-80) cc_final: 0.6771 (ptt-90) outliers start: 85 outliers final: 18 residues processed: 627 average time/residue: 1.6325 time to fit residues: 1207.9657 Evaluate side-chains 540 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 511 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 173 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain H residue 254 ILE Chi-restraints excluded: chain H residue 437 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 0.9980 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: 0.7980 chunk 416 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 532 ASN B 273 ASN B 461 GLN ** 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** ** C 316 ASN ** 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 253 ASN D 398 ASN D 461 GLN ** D 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 HIS ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN F 219 ASN F 275 ASN G 118 GLN G 391 ASN ** G 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN H 129 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36823 Z= 0.217 Angle : 0.579 8.374 50062 Z= 0.307 Chirality : 0.047 0.189 5304 Planarity : 0.005 0.063 6335 Dihedral : 4.535 19.757 4744 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.98 % Allowed : 13.30 % Favored : 84.72 % 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: -1.02 (0.12), residues: 4311 helix: 0.10 (0.13), residues: 1664 sheet: -0.69 (0.18), residues: 904 loop : -1.32 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 448 HIS 0.012 0.001 HIS B 239 PHE 0.025 0.001 PHE A 367 TYR 0.018 0.001 TYR F 334 ARG 0.011 0.001 ARG E 222 *********************** 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 619 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 542 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8267 (p) cc_final: 0.7992 (p) REVERT: A 190 ILE cc_start: 0.8155 (pt) cc_final: 0.7606 (mt) REVERT: A 268 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8289 (ttpt) REVERT: A 587 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8221 (tptm) REVERT: B 186 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7239 (ttm170) REVERT: B 226 PHE cc_start: 0.7674 (m-80) cc_final: 0.7341 (m-80) REVERT: B 351 ARG cc_start: 0.4769 (mmm160) cc_final: 0.4095 (mmm-85) REVERT: B 411 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7299 (pp) REVERT: B 549 GLU cc_start: 0.7338 (tt0) cc_final: 0.6862 (tm-30) REVERT: C 108 PHE cc_start: 0.7448 (p90) cc_final: 0.7127 (p90) REVERT: C 168 LEU cc_start: 0.7835 (mt) cc_final: 0.7511 (mt) REVERT: C 256 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: C 351 ARG cc_start: 0.6170 (mmt180) cc_final: 0.5657 (mmm-85) REVERT: C 373 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 379 ASN cc_start: 0.7210 (OUTLIER) cc_final: 0.6493 (t0) REVERT: C 385 ILE cc_start: 0.8777 (mt) cc_final: 0.8018 (tt) REVERT: C 562 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: D 108 PHE cc_start: 0.7670 (p90) cc_final: 0.7342 (p90) REVERT: D 136 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7213 (p0) REVERT: D 203 LYS cc_start: 0.7720 (ptmm) cc_final: 0.7425 (pttm) REVERT: D 216 GLU cc_start: 0.7421 (tt0) cc_final: 0.7053 (tt0) REVERT: D 347 ILE cc_start: 0.8377 (tp) cc_final: 0.8148 (mt) REVERT: D 362 ARG cc_start: 0.5987 (ttp-110) cc_final: 0.4442 (tpm-80) REVERT: D 535 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: D 627 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7404 (t70) REVERT: E 174 PHE cc_start: 0.8079 (t80) cc_final: 0.7825 (t80) REVERT: E 189 GLN cc_start: 0.7233 (tp40) cc_final: 0.6403 (tm-30) REVERT: E 199 VAL cc_start: 0.7210 (t) cc_final: 0.6896 (p) REVERT: E 283 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: E 351 ARG cc_start: 0.4863 (tpm170) cc_final: 0.2755 (ttt180) REVERT: E 363 ASN cc_start: 0.7236 (m-40) cc_final: 0.6817 (m110) REVERT: E 391 ASN cc_start: 0.7319 (m-40) cc_final: 0.6785 (t0) REVERT: E 420 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7339 (ttpt) REVERT: E 423 LYS cc_start: 0.6802 (tttt) cc_final: 0.6585 (tmtt) REVERT: E 428 ARG cc_start: 0.7419 (tpp80) cc_final: 0.6821 (tpt-90) REVERT: E 481 GLU cc_start: 0.7462 (tp30) cc_final: 0.7226 (tm-30) REVERT: F 173 HIS cc_start: 0.6076 (OUTLIER) cc_final: 0.5831 (m90) REVERT: F 231 ASP cc_start: 0.7822 (t70) cc_final: 0.7491 (t70) REVERT: F 332 LYS cc_start: 0.7981 (mmpt) cc_final: 0.7765 (mmtm) REVERT: F 351 ARG cc_start: 0.5091 (tpm170) cc_final: 0.3759 (tpt-90) REVERT: F 373 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6862 (tp30) REVERT: F 376 PHE cc_start: 0.7313 (m-10) cc_final: 0.6980 (m-10) REVERT: F 381 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7408 (ttpt) REVERT: F 510 PHE cc_start: 0.7880 (m-10) cc_final: 0.7680 (m-80) REVERT: F 585 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7731 (p) REVERT: G 118 GLN cc_start: 0.7097 (pt0) cc_final: 0.6816 (pt0) REVERT: G 189 GLN cc_start: 0.7521 (tp40) cc_final: 0.7210 (tt0) REVERT: G 362 ARG cc_start: 0.5142 (ttm110) cc_final: 0.4020 (tmt170) REVERT: G 622 ASP cc_start: 0.6709 (t0) cc_final: 0.6400 (t0) REVERT: H 120 TYR cc_start: 0.7836 (m-80) cc_final: 0.7621 (m-80) REVERT: H 163 TYR cc_start: 0.7808 (t80) cc_final: 0.7483 (t80) REVERT: H 231 ASP cc_start: 0.7175 (t0) cc_final: 0.6754 (t70) REVERT: H 295 TYR cc_start: 0.8178 (t80) cc_final: 0.7529 (t80) REVERT: H 298 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7086 (t0) REVERT: H 373 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7371 (mm-30) REVERT: H 381 LYS cc_start: 0.7687 (tppt) cc_final: 0.7148 (tppt) REVERT: H 391 ASN cc_start: 0.8267 (m110) cc_final: 0.7946 (t0) REVERT: H 481 GLU cc_start: 0.7504 (tp30) cc_final: 0.7285 (tp30) REVERT: H 566 ARG cc_start: 0.6904 (ptm-80) cc_final: 0.6487 (tmm-80) outliers start: 77 outliers final: 24 residues processed: 583 average time/residue: 1.6587 time to fit residues: 1138.1449 Evaluate side-chains 547 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 510 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain F residue 173 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 3.9990 chunk 290 optimal weight: 0.0270 chunk 200 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 387 optimal weight: 0.5980 chunk 409 optimal weight: 0.4980 chunk 202 optimal weight: 4.9990 chunk 366 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 532 ASN B 220 ASN B 273 ASN B 532 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN E 162 HIS ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN G 391 ASN G 419 ASN H 129 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36823 Z= 0.151 Angle : 0.516 8.084 50062 Z= 0.273 Chirality : 0.045 0.184 5304 Planarity : 0.004 0.054 6335 Dihedral : 4.215 18.869 4744 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 14.59 % Favored : 83.56 % 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: -0.62 (0.12), residues: 4311 helix: 0.50 (0.13), residues: 1680 sheet: -0.49 (0.18), residues: 920 loop : -1.20 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP C 448 HIS 0.009 0.001 HIS C 171 PHE 0.020 0.001 PHE B 108 TYR 0.010 0.001 TYR F 334 ARG 0.012 0.001 ARG E 222 *********************** 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 649 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 577 time to evaluate : 4.293 Fit side-chains revert: symmetry clash REVERT: A 190 ILE cc_start: 0.8099 (pt) cc_final: 0.7606 (mt) REVERT: A 197 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: A 268 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8295 (ttpt) REVERT: A 270 MET cc_start: 0.8673 (mmp) cc_final: 0.8036 (mmt) REVERT: A 347 ILE cc_start: 0.8063 (mt) cc_final: 0.7736 (mp) REVERT: A 420 LYS cc_start: 0.8115 (tppt) cc_final: 0.7868 (tppp) REVERT: B 119 MET cc_start: 0.8326 (ptt) cc_final: 0.7947 (ptt) REVERT: B 186 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7181 (ttm170) REVERT: B 226 PHE cc_start: 0.7474 (m-80) cc_final: 0.7167 (m-80) REVERT: B 351 ARG cc_start: 0.4745 (mmm160) cc_final: 0.4039 (mmm-85) REVERT: B 544 GLU cc_start: 0.7111 (tt0) cc_final: 0.6900 (tp30) REVERT: B 549 GLU cc_start: 0.7314 (tt0) cc_final: 0.6879 (tm-30) REVERT: C 108 PHE cc_start: 0.7455 (p90) cc_final: 0.7127 (p90) REVERT: C 163 TYR cc_start: 0.7736 (t80) cc_final: 0.7360 (t80) REVERT: C 168 LEU cc_start: 0.7923 (mt) cc_final: 0.7592 (mt) REVERT: C 256 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: C 260 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7401 (ttm-80) REVERT: C 351 ARG cc_start: 0.6164 (mmt180) cc_final: 0.5777 (mmm-85) REVERT: C 373 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 378 LYS cc_start: 0.7977 (tppt) cc_final: 0.7473 (mppt) REVERT: C 379 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.7027 (t0) REVERT: C 385 ILE cc_start: 0.8775 (mt) cc_final: 0.8031 (tt) REVERT: D 108 PHE cc_start: 0.7753 (p90) cc_final: 0.7391 (p90) REVERT: D 136 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7283 (p0) REVERT: D 203 LYS cc_start: 0.7719 (ptmm) cc_final: 0.7422 (pttm) REVERT: D 216 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: D 256 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: D 347 ILE cc_start: 0.8349 (tp) cc_final: 0.8117 (mt) REVERT: D 538 ASP cc_start: 0.7421 (t0) cc_final: 0.7220 (p0) REVERT: D 566 ARG cc_start: 0.7205 (ptm-80) cc_final: 0.6992 (ptp90) REVERT: E 174 PHE cc_start: 0.8060 (t80) cc_final: 0.7800 (t80) REVERT: E 189 GLN cc_start: 0.7330 (tp40) cc_final: 0.6498 (tm-30) REVERT: E 199 VAL cc_start: 0.7196 (t) cc_final: 0.6877 (p) REVERT: E 206 PRO cc_start: 0.6195 (Cg_endo) cc_final: 0.5975 (Cg_exo) REVERT: E 283 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: E 351 ARG cc_start: 0.4893 (tpm170) cc_final: 0.2744 (ttt180) REVERT: E 359 HIS cc_start: 0.7254 (t70) cc_final: 0.7024 (t-90) REVERT: E 363 ASN cc_start: 0.7161 (m-40) cc_final: 0.6939 (m-40) REVERT: E 391 ASN cc_start: 0.7301 (m-40) cc_final: 0.6772 (t0) REVERT: E 411 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7504 (mp) REVERT: E 420 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7264 (ttpt) REVERT: E 428 ARG cc_start: 0.7351 (tpp80) cc_final: 0.6719 (tpt-90) REVERT: E 481 GLU cc_start: 0.7426 (tp30) cc_final: 0.7184 (tm-30) REVERT: F 154 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.6172 (mtpp) REVERT: F 173 HIS cc_start: 0.6165 (OUTLIER) cc_final: 0.5944 (m90) REVERT: F 231 ASP cc_start: 0.7793 (t70) cc_final: 0.7522 (t70) REVERT: F 351 ARG cc_start: 0.5210 (tpm170) cc_final: 0.3646 (tpt-90) REVERT: F 373 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6746 (tp30) REVERT: F 376 PHE cc_start: 0.7274 (m-10) cc_final: 0.6898 (m-10) REVERT: F 381 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7362 (ttpt) REVERT: F 510 PHE cc_start: 0.7819 (m-10) cc_final: 0.7616 (m-80) REVERT: F 585 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7673 (p) REVERT: F 603 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8184 (tttm) REVERT: G 189 GLN cc_start: 0.7577 (tp40) cc_final: 0.7249 (tt0) REVERT: G 362 ARG cc_start: 0.5203 (ttm110) cc_final: 0.4175 (tmt170) REVERT: G 420 LYS cc_start: 0.8211 (mppt) cc_final: 0.7646 (mptp) REVERT: G 535 GLN cc_start: 0.7929 (mt0) cc_final: 0.7687 (mt0) REVERT: G 596 ARG cc_start: 0.7505 (ptp-170) cc_final: 0.7208 (ptp-170) REVERT: G 622 ASP cc_start: 0.6658 (t0) cc_final: 0.6304 (t0) REVERT: H 163 TYR cc_start: 0.7722 (t80) cc_final: 0.7316 (t80) REVERT: H 216 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6077 (pp20) REVERT: H 231 ASP cc_start: 0.7036 (t0) cc_final: 0.6708 (t70) REVERT: H 260 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7296 (tmm-80) REVERT: H 295 TYR cc_start: 0.8099 (t80) cc_final: 0.7314 (t80) REVERT: H 373 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7348 (mm-30) REVERT: H 381 LYS cc_start: 0.7649 (tppt) cc_final: 0.7083 (tppt) REVERT: H 391 ASN cc_start: 0.8238 (m110) cc_final: 0.7934 (t0) REVERT: H 481 GLU cc_start: 0.7599 (tp30) cc_final: 0.7279 (tp30) REVERT: H 566 ARG cc_start: 0.6817 (ptm-80) cc_final: 0.6357 (tmm-80) outliers start: 72 outliers final: 15 residues processed: 613 average time/residue: 1.6959 time to fit residues: 1232.9495 Evaluate side-chains 546 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 517 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 173 HIS Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 603 LYS Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 216 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 349 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 0.6980 chunk 367 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 589 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 253 ASN D 398 ASN D 461 GLN E 208 HIS E 220 ASN E 316 ASN E 379 ASN F 219 ASN F 275 ASN F 277 GLN G 118 GLN G 391 ASN H 129 GLN H 164 HIS H 589 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36823 Z= 0.214 Angle : 0.549 8.665 50062 Z= 0.290 Chirality : 0.047 0.184 5304 Planarity : 0.005 0.057 6335 Dihedral : 4.296 18.768 4744 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.40 % Allowed : 14.54 % Favored : 83.07 % 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: -0.49 (0.13), residues: 4311 helix: 0.58 (0.13), residues: 1688 sheet: -0.40 (0.18), residues: 920 loop : -1.10 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 448 HIS 0.014 0.001 HIS D 239 PHE 0.021 0.001 PHE E 121 TYR 0.023 0.001 TYR D 404 ARG 0.013 0.001 ARG F 212 *********************** 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 626 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 533 time to evaluate : 4.220 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8260 (p) cc_final: 0.7951 (p) REVERT: A 190 ILE cc_start: 0.8124 (pt) cc_final: 0.7628 (mt) REVERT: A 216 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7356 (pt0) REVERT: A 270 MET cc_start: 0.8646 (mmp) cc_final: 0.7995 (mmt) REVERT: A 347 ILE cc_start: 0.8060 (mt) cc_final: 0.7720 (mp) REVERT: A 351 ARG cc_start: 0.5312 (mmm160) cc_final: 0.3769 (mmp80) REVERT: B 119 MET cc_start: 0.8266 (ptt) cc_final: 0.7862 (ptt) REVERT: B 186 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7175 (ttm170) REVERT: B 226 PHE cc_start: 0.7616 (m-80) cc_final: 0.7281 (m-80) REVERT: B 549 GLU cc_start: 0.7366 (tt0) cc_final: 0.6874 (tm-30) REVERT: C 108 PHE cc_start: 0.7470 (p90) cc_final: 0.7126 (p90) REVERT: C 163 TYR cc_start: 0.7813 (t80) cc_final: 0.7507 (t80) REVERT: C 168 LEU cc_start: 0.7908 (mt) cc_final: 0.7579 (mt) REVERT: C 173 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6409 (m90) REVERT: C 256 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: C 277 GLN cc_start: 0.8291 (mt0) cc_final: 0.8049 (mt0) REVERT: C 351 ARG cc_start: 0.6200 (mmt180) cc_final: 0.5777 (mmm-85) REVERT: C 373 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7317 (mt-10) REVERT: C 377 ASP cc_start: 0.7431 (t0) cc_final: 0.7193 (t0) REVERT: C 378 LYS cc_start: 0.8018 (tppt) cc_final: 0.7519 (mptp) REVERT: C 379 ASN cc_start: 0.7147 (OUTLIER) cc_final: 0.6433 (t0) REVERT: C 385 ILE cc_start: 0.8777 (mt) cc_final: 0.8496 (mm) REVERT: C 409 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6884 (ttp) REVERT: D 108 PHE cc_start: 0.7728 (p90) cc_final: 0.7384 (p90) REVERT: D 120 TYR cc_start: 0.8021 (m-10) cc_final: 0.7808 (m-80) REVERT: D 136 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7223 (p0) REVERT: D 216 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: D 256 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: D 535 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: D 538 ASP cc_start: 0.7456 (t0) cc_final: 0.7226 (p0) REVERT: E 174 PHE cc_start: 0.8040 (t80) cc_final: 0.7796 (t80) REVERT: E 199 VAL cc_start: 0.7188 (t) cc_final: 0.6866 (p) REVERT: E 206 PRO cc_start: 0.6192 (Cg_endo) cc_final: 0.5991 (Cg_exo) REVERT: E 283 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: E 351 ARG cc_start: 0.5034 (tpm170) cc_final: 0.2866 (ttt180) REVERT: E 359 HIS cc_start: 0.7412 (t70) cc_final: 0.7149 (t-90) REVERT: E 391 ASN cc_start: 0.7283 (m-40) cc_final: 0.6786 (t0) REVERT: E 420 LYS cc_start: 0.7774 (mmmm) cc_final: 0.7231 (ttpt) REVERT: E 428 ARG cc_start: 0.7397 (tpp80) cc_final: 0.6763 (tpt-90) REVERT: E 481 GLU cc_start: 0.7444 (tp30) cc_final: 0.7207 (tm-30) REVERT: F 154 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5679 (pmtt) REVERT: F 173 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.5987 (m90) REVERT: F 231 ASP cc_start: 0.7855 (t70) cc_final: 0.7537 (t70) REVERT: F 277 GLN cc_start: 0.8502 (mt0) cc_final: 0.8226 (mt0) REVERT: F 332 LYS cc_start: 0.7907 (mmpt) cc_final: 0.7641 (mmtm) REVERT: F 351 ARG cc_start: 0.5227 (tpm170) cc_final: 0.3557 (tmt-80) REVERT: F 373 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6727 (tp30) REVERT: F 376 PHE cc_start: 0.7305 (m-10) cc_final: 0.6937 (m-10) REVERT: F 428 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6913 (tpt-90) REVERT: F 535 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: F 585 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (p) REVERT: F 603 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8177 (tttm) REVERT: G 189 GLN cc_start: 0.7602 (tp40) cc_final: 0.7289 (tt0) REVERT: G 197 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: G 212 ARG cc_start: 0.7184 (ttm110) cc_final: 0.6867 (tpp-160) REVERT: G 362 ARG cc_start: 0.5215 (ttm110) cc_final: 0.4189 (tmt170) REVERT: G 622 ASP cc_start: 0.6799 (t0) cc_final: 0.6472 (t0) REVERT: H 167 MET cc_start: 0.6560 (mmt) cc_final: 0.6234 (mtp) REVERT: H 231 ASP cc_start: 0.7137 (t0) cc_final: 0.6822 (t70) REVERT: H 260 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7288 (tmm-80) REVERT: H 295 TYR cc_start: 0.8177 (t80) cc_final: 0.7450 (t80) REVERT: H 298 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7056 (t0) REVERT: H 381 LYS cc_start: 0.7676 (tppt) cc_final: 0.7100 (tppt) REVERT: H 391 ASN cc_start: 0.8213 (m110) cc_final: 0.7855 (t0) REVERT: H 393 MET cc_start: 0.7567 (mtt) cc_final: 0.7352 (mtm) REVERT: H 462 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.8157 (m170) REVERT: H 481 GLU cc_start: 0.7635 (tp30) cc_final: 0.7300 (tp30) REVERT: H 566 ARG cc_start: 0.6868 (ptm-80) cc_final: 0.6468 (tmm-80) outliers start: 93 outliers final: 32 residues processed: 583 average time/residue: 1.6492 time to fit residues: 1134.7813 Evaluate side-chains 555 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 503 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 173 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 603 LYS Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 9.9990 chunk 369 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 410 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** B 220 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN E 208 HIS E 359 HIS E 363 ASN E 379 ASN F 275 ASN F 608 HIS G 118 GLN G 391 ASN H 129 GLN H 162 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36823 Z= 0.271 Angle : 0.586 9.352 50062 Z= 0.310 Chirality : 0.048 0.181 5304 Planarity : 0.005 0.052 6335 Dihedral : 4.489 20.576 4744 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.37 % Allowed : 14.90 % Favored : 82.73 % 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: -0.49 (0.13), residues: 4311 helix: 0.56 (0.13), residues: 1680 sheet: -0.41 (0.18), residues: 904 loop : -1.06 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP C 448 HIS 0.012 0.001 HIS B 239 PHE 0.025 0.002 PHE B 108 TYR 0.015 0.002 TYR D 237 ARG 0.015 0.001 ARG F 212 *********************** 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 613 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 521 time to evaluate : 4.095 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8220 (p) cc_final: 0.7838 (p) REVERT: A 190 ILE cc_start: 0.8114 (pt) cc_final: 0.7620 (mt) REVERT: A 270 MET cc_start: 0.8537 (mmp) cc_final: 0.7854 (mmt) REVERT: A 347 ILE cc_start: 0.8115 (mt) cc_final: 0.7776 (mp) REVERT: A 351 ARG cc_start: 0.5423 (mmm160) cc_final: 0.3792 (mmp80) REVERT: B 186 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7322 (ttm170) REVERT: B 227 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7138 (ptpt) REVERT: B 325 MET cc_start: 0.7186 (tpt) cc_final: 0.6917 (tmm) REVERT: B 398 ASN cc_start: 0.7418 (t0) cc_final: 0.6767 (m-40) REVERT: B 549 GLU cc_start: 0.7343 (tt0) cc_final: 0.6840 (tm-30) REVERT: C 108 PHE cc_start: 0.7367 (p90) cc_final: 0.7064 (p90) REVERT: C 163 TYR cc_start: 0.7801 (t80) cc_final: 0.7464 (t80) REVERT: C 168 LEU cc_start: 0.7885 (mt) cc_final: 0.7578 (mt) REVERT: C 256 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: C 277 GLN cc_start: 0.8325 (mt0) cc_final: 0.8115 (tt0) REVERT: C 373 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 378 LYS cc_start: 0.8030 (tppt) cc_final: 0.7521 (mptp) REVERT: C 379 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6451 (t0) REVERT: C 385 ILE cc_start: 0.8759 (mt) cc_final: 0.8476 (mm) REVERT: C 409 MET cc_start: 0.7234 (mmm) cc_final: 0.6982 (ttp) REVERT: D 108 PHE cc_start: 0.7755 (p90) cc_final: 0.7386 (p90) REVERT: D 120 TYR cc_start: 0.8033 (m-10) cc_final: 0.7826 (m-80) REVERT: D 136 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7179 (p0) REVERT: D 189 GLN cc_start: 0.7518 (tp-100) cc_final: 0.7167 (tt0) REVERT: D 216 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: D 256 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: E 174 PHE cc_start: 0.8039 (t80) cc_final: 0.7655 (t80) REVERT: E 199 VAL cc_start: 0.7177 (t) cc_final: 0.6854 (p) REVERT: E 283 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: E 351 ARG cc_start: 0.5092 (tpm170) cc_final: 0.2811 (ttt180) REVERT: E 373 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7163 (mm-30) REVERT: E 420 LYS cc_start: 0.7761 (mmmm) cc_final: 0.7196 (ttpt) REVERT: E 428 ARG cc_start: 0.7425 (tpp80) cc_final: 0.6841 (tpt-90) REVERT: E 481 GLU cc_start: 0.7476 (tp30) cc_final: 0.7198 (tm-30) REVERT: F 154 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5630 (pmtt) REVERT: F 231 ASP cc_start: 0.7934 (t70) cc_final: 0.7560 (t70) REVERT: F 332 LYS cc_start: 0.7982 (mmpt) cc_final: 0.7726 (mmtm) REVERT: F 351 ARG cc_start: 0.5096 (tpm170) cc_final: 0.3565 (tmt-80) REVERT: F 373 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6743 (tp30) REVERT: F 376 PHE cc_start: 0.7321 (m-10) cc_final: 0.6931 (m-10) REVERT: F 381 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7213 (ttpt) REVERT: F 428 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6936 (tpt-90) REVERT: F 488 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: F 535 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: F 587 LYS cc_start: 0.8037 (tppp) cc_final: 0.7667 (ttpp) REVERT: F 603 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8198 (tttm) REVERT: G 189 GLN cc_start: 0.7583 (tp40) cc_final: 0.7283 (tt0) REVERT: G 212 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6831 (tpp-160) REVERT: G 341 ASP cc_start: 0.7978 (t70) cc_final: 0.7772 (t0) REVERT: G 362 ARG cc_start: 0.5254 (ttm110) cc_final: 0.4172 (tmt170) REVERT: G 420 LYS cc_start: 0.8383 (mppt) cc_final: 0.7767 (mppt) REVERT: H 167 MET cc_start: 0.6640 (mmt) cc_final: 0.6249 (mtp) REVERT: H 295 TYR cc_start: 0.8212 (t80) cc_final: 0.7519 (t80) REVERT: H 298 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7102 (t0) REVERT: H 381 LYS cc_start: 0.7695 (tppt) cc_final: 0.7112 (tppt) REVERT: H 391 ASN cc_start: 0.8225 (m110) cc_final: 0.7875 (t0) REVERT: H 462 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.8165 (m170) REVERT: H 481 GLU cc_start: 0.7686 (tp30) cc_final: 0.7308 (tp30) REVERT: H 566 ARG cc_start: 0.6870 (ptm-80) cc_final: 0.6660 (tmt-80) outliers start: 92 outliers final: 43 residues processed: 575 average time/residue: 1.6518 time to fit residues: 1121.0122 Evaluate side-chains 552 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 494 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 603 LYS Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 610 MET Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 299 optimal weight: 0.2980 chunk 232 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 229 optimal weight: 0.0030 chunk 408 optimal weight: 3.9990 chunk 255 optimal weight: 0.6980 chunk 249 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 C 132 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN E 171 HIS E 208 HIS ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN F 275 ASN F 316 ASN G 118 GLN G 391 ASN H 129 GLN H 162 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36823 Z= 0.147 Angle : 0.512 8.958 50062 Z= 0.269 Chirality : 0.045 0.178 5304 Planarity : 0.004 0.050 6335 Dihedral : 4.174 18.581 4744 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 16.34 % Favored : 82.11 % 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: -0.22 (0.13), residues: 4311 helix: 0.82 (0.13), residues: 1688 sheet: -0.22 (0.18), residues: 912 loop : -0.99 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP C 448 HIS 0.008 0.001 HIS C 171 PHE 0.021 0.001 PHE A 108 TYR 0.022 0.001 TYR D 404 ARG 0.019 0.000 ARG E 222 *********************** 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 595 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 535 time to evaluate : 4.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8175 (p) cc_final: 0.7780 (p) REVERT: A 190 ILE cc_start: 0.7998 (pt) cc_final: 0.7568 (mt) REVERT: A 216 GLU cc_start: 0.7416 (pt0) cc_final: 0.7183 (tt0) REVERT: A 347 ILE cc_start: 0.7946 (mt) cc_final: 0.7665 (mp) REVERT: A 351 ARG cc_start: 0.5406 (mmm160) cc_final: 0.3808 (mmp80) REVERT: A 420 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7844 (tppp) REVERT: A 607 LYS cc_start: 0.8380 (tppt) cc_final: 0.7908 (tppt) REVERT: B 119 MET cc_start: 0.8307 (ptt) cc_final: 0.7625 (ptt) REVERT: B 186 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7258 (ttm170) REVERT: B 226 PHE cc_start: 0.7526 (m-80) cc_final: 0.7214 (m-80) REVERT: B 227 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7046 (ptpt) REVERT: B 325 MET cc_start: 0.7115 (tpt) cc_final: 0.6841 (tmm) REVERT: B 348 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8372 (pt) REVERT: B 351 ARG cc_start: 0.4510 (mmm160) cc_final: 0.3398 (mmm-85) REVERT: B 398 ASN cc_start: 0.7399 (t0) cc_final: 0.6757 (m-40) REVERT: B 549 GLU cc_start: 0.7356 (tt0) cc_final: 0.6915 (tm-30) REVERT: C 108 PHE cc_start: 0.7356 (p90) cc_final: 0.7045 (p90) REVERT: C 168 LEU cc_start: 0.7974 (mt) cc_final: 0.7661 (mt) REVERT: C 194 LYS cc_start: 0.7433 (tptp) cc_final: 0.7190 (ptmm) REVERT: C 351 ARG cc_start: 0.4950 (mtp85) cc_final: 0.3976 (mmm-85) REVERT: C 373 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 378 LYS cc_start: 0.7947 (tppt) cc_final: 0.7394 (mptp) REVERT: C 385 ILE cc_start: 0.8715 (mt) cc_final: 0.8461 (mm) REVERT: D 108 PHE cc_start: 0.7805 (p90) cc_final: 0.7435 (p90) REVERT: D 136 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7196 (p0) REVERT: D 216 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: D 256 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: D 538 ASP cc_start: 0.7454 (t0) cc_final: 0.7218 (p0) REVERT: E 174 PHE cc_start: 0.8021 (t80) cc_final: 0.7771 (t80) REVERT: E 199 VAL cc_start: 0.7151 (t) cc_final: 0.6821 (p) REVERT: E 283 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: E 351 ARG cc_start: 0.4998 (tpm170) cc_final: 0.2743 (ttt180) REVERT: E 420 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7186 (ttpt) REVERT: E 428 ARG cc_start: 0.7318 (tpp80) cc_final: 0.6754 (tpt-90) REVERT: E 481 GLU cc_start: 0.7439 (tp30) cc_final: 0.7191 (tm-30) REVERT: E 610 MET cc_start: 0.7835 (ttt) cc_final: 0.7632 (tpp) REVERT: F 154 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6117 (ttpp) REVERT: F 212 ARG cc_start: 0.6475 (mmp-170) cc_final: 0.6120 (mmm160) REVERT: F 231 ASP cc_start: 0.7828 (t70) cc_final: 0.7526 (t70) REVERT: F 284 MET cc_start: 0.8684 (mtt) cc_final: 0.8457 (mtt) REVERT: F 351 ARG cc_start: 0.5016 (tpm170) cc_final: 0.3399 (tmt-80) REVERT: F 373 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6730 (tp30) REVERT: F 376 PHE cc_start: 0.7203 (m-10) cc_final: 0.6811 (m-10) REVERT: F 381 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7223 (ttpt) REVERT: G 189 GLN cc_start: 0.7622 (tp40) cc_final: 0.7303 (tt0) REVERT: G 212 ARG cc_start: 0.7086 (ttm110) cc_final: 0.6787 (tpp-160) REVERT: G 298 ASP cc_start: 0.7384 (t0) cc_final: 0.7148 (m-30) REVERT: G 362 ARG cc_start: 0.5204 (ttm110) cc_final: 0.4184 (tmt170) REVERT: G 377 ASP cc_start: 0.7445 (t0) cc_final: 0.7157 (t0) REVERT: G 420 LYS cc_start: 0.8339 (mppt) cc_final: 0.7313 (mttm) REVERT: G 535 GLN cc_start: 0.7937 (mt0) cc_final: 0.7700 (mt0) REVERT: G 622 ASP cc_start: 0.6676 (t0) cc_final: 0.6371 (t0) REVERT: H 121 PHE cc_start: 0.8041 (t80) cc_final: 0.7767 (t80) REVERT: H 167 MET cc_start: 0.6467 (mmt) cc_final: 0.6254 (mtp) REVERT: H 295 TYR cc_start: 0.8119 (t80) cc_final: 0.7391 (t80) REVERT: H 298 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7130 (t0) REVERT: H 373 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7353 (mm-30) REVERT: H 381 LYS cc_start: 0.7660 (tppt) cc_final: 0.7083 (tppt) REVERT: H 391 ASN cc_start: 0.8244 (m110) cc_final: 0.7917 (t0) REVERT: H 420 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7469 (mmpt) REVERT: H 462 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8028 (m170) REVERT: H 481 GLU cc_start: 0.7705 (tp30) cc_final: 0.7288 (tp30) REVERT: H 566 ARG cc_start: 0.6817 (ptm-80) cc_final: 0.6567 (tmt-80) outliers start: 60 outliers final: 27 residues processed: 568 average time/residue: 1.6175 time to fit residues: 1087.6019 Evaluate side-chains 534 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 496 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 535 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 316 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN E 208 HIS E 379 ASN F 275 ASN F 391 ASN G 391 ASN H 129 GLN H 162 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3099 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= 0.251 Angle : 0.571 11.636 50062 Z= 0.300 Chirality : 0.048 0.192 5304 Planarity : 0.005 0.058 6335 Dihedral : 4.360 18.493 4744 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.93 % Allowed : 16.21 % Favored : 81.86 % 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: -0.29 (0.13), residues: 4311 helix: 0.73 (0.13), residues: 1712 sheet: -0.23 (0.18), residues: 896 loop : -1.03 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 448 HIS 0.011 0.001 HIS A 239 PHE 0.029 0.002 PHE A 108 TYR 0.020 0.001 TYR F 334 ARG 0.014 0.001 ARG F 566 *********************** 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 572 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 497 time to evaluate : 4.049 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8089 (p) cc_final: 0.7747 (p) REVERT: A 190 ILE cc_start: 0.8058 (pt) cc_final: 0.7611 (mt) REVERT: A 216 GLU cc_start: 0.7416 (pt0) cc_final: 0.7211 (tt0) REVERT: A 231 ASP cc_start: 0.8036 (t0) cc_final: 0.7810 (t0) REVERT: A 347 ILE cc_start: 0.8038 (mt) cc_final: 0.7705 (mp) REVERT: A 351 ARG cc_start: 0.5503 (mmm160) cc_final: 0.3830 (mmp80) REVERT: A 420 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (tppp) REVERT: A 607 LYS cc_start: 0.8384 (tppt) cc_final: 0.7911 (tppt) REVERT: B 186 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7231 (ttm170) REVERT: B 226 PHE cc_start: 0.7669 (m-80) cc_final: 0.7317 (m-80) REVERT: B 227 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7103 (ptpt) REVERT: B 348 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8358 (pt) REVERT: B 398 ASN cc_start: 0.7513 (t0) cc_final: 0.6912 (m-40) REVERT: C 108 PHE cc_start: 0.7333 (p90) cc_final: 0.7028 (p90) REVERT: C 168 LEU cc_start: 0.7762 (mt) cc_final: 0.7465 (mt) REVERT: C 173 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.6348 (m90) REVERT: C 194 LYS cc_start: 0.7406 (tptp) cc_final: 0.7193 (ptmm) REVERT: C 351 ARG cc_start: 0.5146 (mtp85) cc_final: 0.4085 (mmm-85) REVERT: C 373 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7409 (mt-10) REVERT: C 378 LYS cc_start: 0.8061 (tppt) cc_final: 0.7437 (mptp) REVERT: C 379 ASN cc_start: 0.7098 (OUTLIER) cc_final: 0.6725 (t0) REVERT: C 385 ILE cc_start: 0.8729 (mt) cc_final: 0.8454 (mm) REVERT: C 562 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6354 (pp20) REVERT: D 108 PHE cc_start: 0.7797 (p90) cc_final: 0.7419 (p90) REVERT: D 136 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7150 (p0) REVERT: D 189 GLN cc_start: 0.7487 (tp-100) cc_final: 0.7126 (tt0) REVERT: D 216 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: D 256 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: D 538 ASP cc_start: 0.7477 (t0) cc_final: 0.7220 (p0) REVERT: E 174 PHE cc_start: 0.8074 (t80) cc_final: 0.7815 (t80) REVERT: E 199 VAL cc_start: 0.7157 (t) cc_final: 0.6822 (p) REVERT: E 283 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: E 351 ARG cc_start: 0.5118 (tpm170) cc_final: 0.2839 (ttt180) REVERT: E 420 LYS cc_start: 0.7860 (mmmm) cc_final: 0.7179 (ttpt) REVERT: E 428 ARG cc_start: 0.7370 (tpp80) cc_final: 0.6814 (tpt-90) REVERT: E 481 GLU cc_start: 0.7453 (tp30) cc_final: 0.7200 (tm-30) REVERT: E 610 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7595 (tpp) REVERT: F 154 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.5644 (pmtt) REVERT: F 212 ARG cc_start: 0.6511 (mmp-170) cc_final: 0.6140 (mmm160) REVERT: F 231 ASP cc_start: 0.7913 (t70) cc_final: 0.7586 (t70) REVERT: F 332 LYS cc_start: 0.7940 (mmpt) cc_final: 0.7691 (mmtm) REVERT: F 351 ARG cc_start: 0.5033 (tpm170) cc_final: 0.3523 (tmt-80) REVERT: F 373 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6665 (tp30) REVERT: F 376 PHE cc_start: 0.7335 (m-10) cc_final: 0.6900 (m-10) REVERT: F 381 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7164 (ttpt) REVERT: F 486 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7706 (mtp85) REVERT: F 535 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: F 587 LYS cc_start: 0.7949 (tppp) cc_final: 0.7609 (ttpp) REVERT: G 189 GLN cc_start: 0.7585 (tp40) cc_final: 0.7258 (tt0) REVERT: G 212 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6854 (tpp-160) REVERT: G 362 ARG cc_start: 0.5226 (ttm110) cc_final: 0.4176 (tmt170) REVERT: G 377 ASP cc_start: 0.7426 (t0) cc_final: 0.7134 (t0) REVERT: H 167 MET cc_start: 0.6507 (mmt) cc_final: 0.6118 (mtp) REVERT: H 295 TYR cc_start: 0.8216 (t80) cc_final: 0.7508 (t80) REVERT: H 298 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7103 (t0) REVERT: H 381 LYS cc_start: 0.7682 (tppt) cc_final: 0.7093 (tppt) REVERT: H 390 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: H 391 ASN cc_start: 0.8274 (m110) cc_final: 0.7834 (t0) REVERT: H 419 ASN cc_start: 0.6982 (m110) cc_final: 0.6619 (m110) REVERT: H 462 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8148 (m170) REVERT: H 481 GLU cc_start: 0.7673 (tp30) cc_final: 0.7246 (tp30) REVERT: H 566 ARG cc_start: 0.6864 (ptm-80) cc_final: 0.6550 (tmt-80) outliers start: 75 outliers final: 33 residues processed: 539 average time/residue: 1.6444 time to fit residues: 1045.3393 Evaluate side-chains 536 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 486 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 596 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 610 MET Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 433 LYS Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 595 THR 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: 0.0770 chunk 357 optimal weight: 1.9990 chunk 380 optimal weight: 0.0030 chunk 229 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 overall best weight: 1.8154 ------------------------------------------------------------------------------- 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 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN E 208 HIS E 379 ASN F 391 ASN G 118 GLN G 391 ASN H 129 GLN H 162 HIS H 535 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36823 Z= 0.256 Angle : 0.582 9.482 50062 Z= 0.306 Chirality : 0.048 0.202 5304 Planarity : 0.005 0.060 6335 Dihedral : 4.440 19.705 4744 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.86 % Allowed : 16.62 % Favored : 81.52 % 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: -0.35 (0.12), residues: 4311 helix: 0.65 (0.13), residues: 1712 sheet: -0.27 (0.18), residues: 896 loop : -1.03 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 448 HIS 0.011 0.001 HIS A 239 PHE 0.030 0.002 PHE A 108 TYR 0.029 0.001 TYR D 404 ARG 0.015 0.001 ARG F 566 *********************** 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 563 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 491 time to evaluate : 4.080 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8102 (p) cc_final: 0.7664 (p) REVERT: A 190 ILE cc_start: 0.8030 (pt) cc_final: 0.7615 (mt) REVERT: A 231 ASP cc_start: 0.8095 (t0) cc_final: 0.7858 (t0) REVERT: A 347 ILE cc_start: 0.8051 (mt) cc_final: 0.7718 (mp) REVERT: A 351 ARG cc_start: 0.5445 (mmm160) cc_final: 0.3783 (mmp80) REVERT: A 420 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7882 (tppp) REVERT: A 607 LYS cc_start: 0.8392 (tppt) cc_final: 0.8186 (tptt) REVERT: B 186 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7240 (ttm170) REVERT: B 227 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7054 (ptpt) REVERT: B 348 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8392 (pt) REVERT: B 351 ARG cc_start: 0.4461 (mmm160) cc_final: 0.3379 (mmm-85) REVERT: B 398 ASN cc_start: 0.7531 (t0) cc_final: 0.6939 (m-40) REVERT: C 108 PHE cc_start: 0.7346 (p90) cc_final: 0.7048 (p90) REVERT: C 168 LEU cc_start: 0.7897 (mt) cc_final: 0.7590 (mt) REVERT: C 173 HIS cc_start: 0.6560 (OUTLIER) cc_final: 0.6313 (m90) REVERT: C 351 ARG cc_start: 0.5160 (mtp85) cc_final: 0.4068 (mmm-85) REVERT: C 373 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 378 LYS cc_start: 0.8059 (tppt) cc_final: 0.7435 (mptp) REVERT: C 379 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6429 (t0) REVERT: C 385 ILE cc_start: 0.8727 (mt) cc_final: 0.8451 (mm) REVERT: C 562 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6333 (pp20) REVERT: D 108 PHE cc_start: 0.7782 (p90) cc_final: 0.7392 (p90) REVERT: D 136 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7141 (p0) REVERT: D 167 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.8002 (mpt) REVERT: D 189 GLN cc_start: 0.7488 (tp-100) cc_final: 0.7140 (tt0) REVERT: D 216 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: D 256 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: D 538 ASP cc_start: 0.7484 (t0) cc_final: 0.7231 (p0) REVERT: E 174 PHE cc_start: 0.8105 (t80) cc_final: 0.7851 (t80) REVERT: E 283 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: E 351 ARG cc_start: 0.5225 (tpm170) cc_final: 0.2973 (ttt180) REVERT: E 373 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7102 (mm-30) REVERT: E 420 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7198 (ttpt) REVERT: E 428 ARG cc_start: 0.7358 (tpp80) cc_final: 0.6833 (tpt-90) REVERT: E 481 GLU cc_start: 0.7456 (tp30) cc_final: 0.7196 (tm-30) REVERT: E 610 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7591 (tpp) REVERT: F 154 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.5556 (pmtt) REVERT: F 212 ARG cc_start: 0.6565 (mmp-170) cc_final: 0.6120 (mmm160) REVERT: F 231 ASP cc_start: 0.7906 (t70) cc_final: 0.7579 (t70) REVERT: F 332 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7700 (mmtm) REVERT: F 351 ARG cc_start: 0.5142 (tpm170) cc_final: 0.3609 (tmt-80) REVERT: F 373 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6681 (tp30) REVERT: F 376 PHE cc_start: 0.7286 (m-10) cc_final: 0.6829 (m-10) REVERT: F 486 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7738 (mtp85) REVERT: F 488 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: F 535 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: F 587 LYS cc_start: 0.7997 (tppp) cc_final: 0.7665 (ttpp) REVERT: G 189 GLN cc_start: 0.7579 (tp40) cc_final: 0.7248 (tt0) REVERT: G 212 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6862 (tpp-160) REVERT: G 298 ASP cc_start: 0.7333 (t0) cc_final: 0.7066 (m-30) REVERT: G 362 ARG cc_start: 0.5186 (ttm110) cc_final: 0.4149 (tmt170) REVERT: G 420 LYS cc_start: 0.8397 (mppt) cc_final: 0.7407 (mttm) REVERT: H 138 ARG cc_start: 0.7117 (mtp180) cc_final: 0.6801 (mtp180) REVERT: H 295 TYR cc_start: 0.8221 (t80) cc_final: 0.7572 (t80) REVERT: H 298 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7120 (t0) REVERT: H 381 LYS cc_start: 0.7677 (tppt) cc_final: 0.7094 (tppt) REVERT: H 390 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: H 391 ASN cc_start: 0.8287 (m110) cc_final: 0.7854 (t0) REVERT: H 419 ASN cc_start: 0.6982 (m110) cc_final: 0.6602 (m110) REVERT: H 462 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8141 (m170) REVERT: H 481 GLU cc_start: 0.7675 (tp30) cc_final: 0.7260 (tp30) REVERT: H 566 ARG cc_start: 0.6894 (ptm-80) cc_final: 0.6579 (tmt-80) outliers start: 72 outliers final: 37 residues processed: 530 average time/residue: 1.6491 time to fit residues: 1039.1416 Evaluate side-chains 537 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 481 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 610 MET Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 chunk 245 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 422 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 chunk 206 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN E 208 HIS E 379 ASN F 391 ASN G 118 GLN G 391 ASN H 127 HIS H 129 GLN H 162 HIS H 535 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36823 Z= 0.241 Angle : 0.572 9.593 50062 Z= 0.301 Chirality : 0.047 0.185 5304 Planarity : 0.005 0.062 6335 Dihedral : 4.437 19.170 4744 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.60 % Allowed : 17.06 % Favored : 81.34 % 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: -0.33 (0.13), residues: 4311 helix: 0.66 (0.13), residues: 1720 sheet: -0.28 (0.18), residues: 896 loop : -1.00 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 448 HIS 0.011 0.001 HIS A 239 PHE 0.030 0.002 PHE A 108 TYR 0.027 0.001 TYR D 404 ARG 0.015 0.001 ARG F 566 ********************** 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: 62 poor density : 490 time to evaluate : 4.409 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8083 (p) cc_final: 0.7655 (p) REVERT: A 190 ILE cc_start: 0.7951 (pt) cc_final: 0.7568 (mt) REVERT: A 231 ASP cc_start: 0.8091 (t0) cc_final: 0.7843 (t0) REVERT: A 270 MET cc_start: 0.8616 (mmp) cc_final: 0.8048 (mmt) REVERT: A 347 ILE cc_start: 0.8058 (mt) cc_final: 0.7722 (mp) REVERT: A 351 ARG cc_start: 0.5440 (mmm160) cc_final: 0.3760 (mmp80) REVERT: A 420 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7882 (tppp) REVERT: A 607 LYS cc_start: 0.8373 (tppt) cc_final: 0.8169 (tptt) REVERT: B 186 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7216 (ttm170) REVERT: B 227 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7038 (ptpt) REVERT: B 348 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8400 (pt) REVERT: B 351 ARG cc_start: 0.4546 (mmm160) cc_final: 0.3426 (mmm-85) REVERT: B 398 ASN cc_start: 0.7485 (t0) cc_final: 0.6968 (m-40) REVERT: C 108 PHE cc_start: 0.7357 (p90) cc_final: 0.7055 (p90) REVERT: C 173 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.6327 (m90) REVERT: C 351 ARG cc_start: 0.5151 (mtp85) cc_final: 0.4083 (mmm-85) REVERT: C 373 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 378 LYS cc_start: 0.8055 (tppt) cc_final: 0.7412 (mptp) REVERT: C 379 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6432 (t0) REVERT: C 385 ILE cc_start: 0.8730 (mt) cc_final: 0.8454 (mm) REVERT: C 562 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6333 (pp20) REVERT: D 108 PHE cc_start: 0.7783 (p90) cc_final: 0.7358 (p90) REVERT: D 136 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7201 (p0) REVERT: D 189 GLN cc_start: 0.7458 (tp-100) cc_final: 0.7098 (tt0) REVERT: D 216 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: D 256 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: D 390 GLU cc_start: 0.7870 (pm20) cc_final: 0.7659 (pm20) REVERT: D 538 ASP cc_start: 0.7502 (t0) cc_final: 0.7237 (p0) REVERT: E 174 PHE cc_start: 0.8098 (t80) cc_final: 0.7840 (t80) REVERT: E 283 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: E 351 ARG cc_start: 0.5122 (tpm170) cc_final: 0.2942 (ttt180) REVERT: E 373 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7164 (mm-30) REVERT: E 420 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7205 (ttpt) REVERT: E 428 ARG cc_start: 0.7403 (tpp80) cc_final: 0.6877 (tpt-90) REVERT: E 481 GLU cc_start: 0.7461 (tp30) cc_final: 0.7219 (tm-30) REVERT: E 610 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7584 (tpp) REVERT: F 154 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5473 (pmtt) REVERT: F 212 ARG cc_start: 0.6621 (mmp-170) cc_final: 0.6180 (mmm160) REVERT: F 231 ASP cc_start: 0.7905 (t70) cc_final: 0.7580 (t70) REVERT: F 332 LYS cc_start: 0.7963 (mmpt) cc_final: 0.7723 (mmtm) REVERT: F 351 ARG cc_start: 0.5176 (tpm170) cc_final: 0.3615 (tmt-80) REVERT: F 353 ASN cc_start: 0.8239 (m-40) cc_final: 0.7796 (m110) REVERT: F 373 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6681 (tp30) REVERT: F 376 PHE cc_start: 0.7365 (m-10) cc_final: 0.6855 (m-10) REVERT: F 381 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7220 (ttpt) REVERT: F 486 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7745 (mtp85) REVERT: F 488 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: F 535 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: F 587 LYS cc_start: 0.7966 (tppp) cc_final: 0.7681 (ttpp) REVERT: G 189 GLN cc_start: 0.7589 (tp40) cc_final: 0.7251 (tt0) REVERT: G 212 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6860 (tpp-160) REVERT: G 298 ASP cc_start: 0.7397 (t0) cc_final: 0.7152 (m-30) REVERT: G 362 ARG cc_start: 0.5168 (ttm110) cc_final: 0.4145 (tmt170) REVERT: G 420 LYS cc_start: 0.8383 (mppt) cc_final: 0.7361 (mttm) REVERT: G 610 MET cc_start: 0.7686 (mtp) cc_final: 0.7261 (ttt) REVERT: H 138 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6728 (mtp180) REVERT: H 167 MET cc_start: 0.6429 (mmt) cc_final: 0.6181 (mtp) REVERT: H 173 HIS cc_start: 0.5935 (m90) cc_final: 0.5691 (m170) REVERT: H 295 TYR cc_start: 0.8208 (t80) cc_final: 0.7544 (t80) REVERT: H 298 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7142 (t0) REVERT: H 373 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7308 (mm-30) REVERT: H 381 LYS cc_start: 0.7688 (tppt) cc_final: 0.7115 (tppt) REVERT: H 390 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: H 391 ASN cc_start: 0.8237 (m110) cc_final: 0.7781 (t0) REVERT: H 419 ASN cc_start: 0.6956 (m110) cc_final: 0.6577 (m110) REVERT: H 462 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.8135 (m170) REVERT: H 481 GLU cc_start: 0.7669 (tp30) cc_final: 0.7377 (tp30) REVERT: H 566 ARG cc_start: 0.6853 (ptm-80) cc_final: 0.6638 (tmt-80) outliers start: 62 outliers final: 39 residues processed: 522 average time/residue: 1.6765 time to fit residues: 1028.6080 Evaluate side-chains 538 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 481 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 596 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 610 MET Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 565 ILE Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 0.0870 chunk 358 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 310 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 345 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.2164 ------------------------------------------------------------------------------- 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 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 239 HIS G 118 GLN G 391 ASN H 129 GLN H 162 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106420 restraints weight = 166671.224| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.69 r_work: 0.2924 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 36823 Z= 0.301 Angle : 0.617 11.202 50062 Z= 0.325 Chirality : 0.049 0.195 5304 Planarity : 0.005 0.063 6335 Dihedral : 4.601 20.828 4744 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.88 % Allowed : 17.01 % Favored : 81.11 % 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: -0.45 (0.12), residues: 4311 helix: 0.54 (0.12), residues: 1720 sheet: -0.34 (0.18), residues: 896 loop : -1.05 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP C 448 HIS 0.012 0.001 HIS A 239 PHE 0.034 0.002 PHE B 108 TYR 0.025 0.002 TYR F 334 ARG 0.015 0.001 ARG F 566 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16594.50 seconds wall clock time: 294 minutes 7.05 seconds (17647.05 seconds total)