Starting phenix.real_space_refine on Tue Feb 20 09:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/02_2024/7azp_11950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/02_2024/7azp_11950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/02_2024/7azp_11950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/02_2024/7azp_11950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/02_2024/7azp_11950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/02_2024/7azp_11950.pdb" } resolution = 3.5 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= 0.010 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 98 5.16 5 C 17178 2.51 5 N 4676 2.21 5 O 5439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F GLU 387": "OE1" <-> "OE2" Residue "F GLU 407": "OE1" <-> "OE2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G GLU 236": "OE1" <-> "OE2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "G GLU 366": "OE1" <-> "OE2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "G GLU 408": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27391 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain: "D" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain: "E" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain: "F" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain: "G" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3913 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 15, 'TRANS': 509} Time building chain proxies: 13.92, per 1000 atoms: 0.51 Number of scatterers: 27391 At special positions: 0 Unit cell: (159.75, 162.945, 89.46, 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 98 16.00 O 5439 8.00 N 4676 7.00 C 17178 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: 10.46 Conformation dependent library (CDL) restraints added in 5.2 seconds 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 49 sheets defined 58.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.829A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 107 removed outlier: 4.152A pdb=" N THR A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.638A pdb=" N ILE A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.594A pdb=" N LEU A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.511A pdb=" N GLU A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 removed outlier: 3.718A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 removed outlier: 4.239A pdb=" N GLU A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.832A pdb=" N LEU A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 4.426A pdb=" N SER A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 428' Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.565A pdb=" N ILE A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.504A pdb=" N LYS A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 496 through 516 Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.828A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 107 removed outlier: 4.152A pdb=" N THR B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.638A pdb=" N ILE B 203 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.594A pdb=" N LEU B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 337 through 355 removed outlier: 3.511A pdb=" N GLU B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.717A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 removed outlier: 4.240A pdb=" N GLU B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.831A pdb=" N LEU B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 428 removed outlier: 4.427A pdb=" N SER B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 428' Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.565A pdb=" N ILE B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 457 Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.504A pdb=" N LYS B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 496 through 516 Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 58 Processing helix chain 'C' and resid 62 through 77 removed outlier: 3.829A pdb=" N VAL C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 removed outlier: 4.152A pdb=" N THR C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.638A pdb=" N ILE C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 241 removed outlier: 3.593A pdb=" N LEU C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 337 through 355 removed outlier: 3.512A pdb=" N GLU C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 removed outlier: 3.717A pdb=" N LEU C 371 " --> pdb=" O ARG C 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.239A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.831A pdb=" N LEU C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 4.426A pdb=" N SER C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 423 through 428' Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.565A pdb=" N ILE C 439 " --> pdb=" O GLN C 435 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 460 through 471 removed outlier: 3.503A pdb=" N LYS C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 496 through 516 Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 20 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 58 Processing helix chain 'D' and resid 62 through 77 removed outlier: 3.828A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 107 removed outlier: 4.152A pdb=" N THR D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 153 through 168 Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.639A pdb=" N ILE D 203 " --> pdb=" O PRO D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 removed outlier: 3.594A pdb=" N LEU D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 337 through 355 removed outlier: 3.512A pdb=" N GLU D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 373 removed outlier: 3.717A pdb=" N LEU D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 409 removed outlier: 4.240A pdb=" N GLU D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.830A pdb=" N LEU D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 4.426A pdb=" N SER D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 428' Processing helix chain 'D' and resid 432 through 446 removed outlier: 3.565A pdb=" N ILE D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 457 Processing helix chain 'D' and resid 460 through 471 removed outlier: 3.503A pdb=" N LYS D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 496 through 516 Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU E 20 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 Processing helix chain 'E' and resid 62 through 77 removed outlier: 3.828A pdb=" N VAL E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 107 removed outlier: 4.152A pdb=" N THR E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.639A pdb=" N ILE E 203 " --> pdb=" O PRO E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 241 removed outlier: 3.593A pdb=" N LEU E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 279 through 295 Processing helix chain 'E' and resid 337 through 355 removed outlier: 3.511A pdb=" N GLU E 342 " --> pdb=" O LYS E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 373 removed outlier: 3.718A pdb=" N LEU E 371 " --> pdb=" O ARG E 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP E 373 " --> pdb=" O ALA E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 removed outlier: 4.240A pdb=" N GLU E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU E 408 " --> pdb=" O ALA E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 421 removed outlier: 3.830A pdb=" N LEU E 419 " --> pdb=" O GLY E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 4.427A pdb=" N SER E 427 " --> pdb=" O PRO E 423 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 423 through 428' Processing helix chain 'E' and resid 432 through 446 removed outlier: 3.564A pdb=" N ILE E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 457 Processing helix chain 'E' and resid 460 through 471 removed outlier: 3.504A pdb=" N LYS E 467 " --> pdb=" O LEU E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 496 through 516 Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU F 20 " --> pdb=" O GLN F 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 58 Processing helix chain 'F' and resid 62 through 77 removed outlier: 3.828A pdb=" N VAL F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 107 removed outlier: 4.152A pdb=" N THR F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 153 through 168 Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.639A pdb=" N ILE F 203 " --> pdb=" O PRO F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 241 removed outlier: 3.594A pdb=" N LEU F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 237 " --> pdb=" O PRO F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 279 through 295 Processing helix chain 'F' and resid 337 through 355 removed outlier: 3.511A pdb=" N GLU F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 373 removed outlier: 3.718A pdb=" N LEU F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 removed outlier: 4.238A pdb=" N GLU F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU F 408 " --> pdb=" O ALA F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.831A pdb=" N LEU F 419 " --> pdb=" O GLY F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 428 removed outlier: 4.426A pdb=" N SER F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 423 through 428' Processing helix chain 'F' and resid 432 through 446 removed outlier: 3.565A pdb=" N ILE F 439 " --> pdb=" O GLN F 435 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE F 442 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 457 Processing helix chain 'F' and resid 460 through 471 removed outlier: 3.503A pdb=" N LYS F 467 " --> pdb=" O LEU F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 491 Processing helix chain 'F' and resid 496 through 516 Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.925A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 58 Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.829A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 107 removed outlier: 4.151A pdb=" N THR G 89 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 153 through 168 Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.639A pdb=" N ILE G 203 " --> pdb=" O PRO G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 241 removed outlier: 3.594A pdb=" N LEU G 235 " --> pdb=" O ILE G 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G 237 " --> pdb=" O PRO G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 279 through 295 Processing helix chain 'G' and resid 337 through 355 removed outlier: 3.512A pdb=" N GLU G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 373 removed outlier: 3.718A pdb=" N LEU G 371 " --> pdb=" O ARG G 367 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 373 " --> pdb=" O ALA G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 409 removed outlier: 4.239A pdb=" N GLU G 390 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU G 407 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU G 408 " --> pdb=" O ALA G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 421 removed outlier: 3.831A pdb=" N LEU G 419 " --> pdb=" O GLY G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 428 removed outlier: 4.426A pdb=" N SER G 427 " --> pdb=" O PRO G 423 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 423 through 428' Processing helix chain 'G' and resid 432 through 446 removed outlier: 3.565A pdb=" N ILE G 439 " --> pdb=" O GLN G 435 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE G 442 " --> pdb=" O GLY G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 457 Processing helix chain 'G' and resid 460 through 471 removed outlier: 3.504A pdb=" N LYS G 467 " --> pdb=" O LEU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 496 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.466A pdb=" N ILE A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLU G 522 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY A 334 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY A 334 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 225 through 226 removed outlier: 4.135A pdb=" N ASP A 253 " --> pdb=" O ILE A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.520A pdb=" N ASP A 483 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AB2, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR B 217 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 248 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 219 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 225 through 226 removed outlier: 4.136A pdb=" N ASP B 253 " --> pdb=" O ILE B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB6, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.520A pdb=" N ASP B 483 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AB8, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY C 334 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY C 334 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR C 217 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 248 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 219 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.135A pdb=" N ASP C 253 " --> pdb=" O ILE C 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.520A pdb=" N ASP C 483 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 2 through 6 Processing sheet with id=AC6, first strand: chain 'D' and resid 173 through 177 Processing sheet with id=AC7, first strand: chain 'D' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY D 334 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY D 334 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR D 217 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE D 248 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 219 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 225 through 226 removed outlier: 4.136A pdb=" N ASP D 253 " --> pdb=" O ILE D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AD2, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.520A pdb=" N ASP D 483 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AD4, first strand: chain 'E' and resid 173 through 177 Processing sheet with id=AD5, first strand: chain 'E' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY E 334 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY E 334 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR E 217 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE E 248 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 219 " --> pdb=" O ILE E 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 225 through 226 removed outlier: 4.135A pdb=" N ASP E 253 " --> pdb=" O ILE E 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AD9, first strand: chain 'E' and resid 475 through 478 removed outlier: 3.520A pdb=" N ASP E 483 " --> pdb=" O ASP E 478 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AE2, first strand: chain 'F' and resid 173 through 177 Processing sheet with id=AE3, first strand: chain 'F' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY F 334 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY F 334 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR F 217 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE F 248 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU F 219 " --> pdb=" O ILE F 248 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 225 through 226 removed outlier: 4.135A pdb=" N ASP F 253 " --> pdb=" O ILE F 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AE7, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.520A pdb=" N ASP F 483 " --> pdb=" O ASP F 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 173 through 177 Processing sheet with id=AE9, first strand: chain 'G' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY G 334 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 190 through 193 removed outlier: 6.059A pdb=" N GLY G 334 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 225 through 226 removed outlier: 4.135A pdb=" N ASP G 253 " --> pdb=" O ILE G 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AF4, first strand: chain 'G' and resid 475 through 478 removed outlier: 3.521A pdb=" N ASP G 483 " --> pdb=" O ASP G 478 " (cutoff:3.500A) 1790 hydrogen bonds defined for protein. 5202 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: 10.51 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9303 1.34 - 1.46: 3148 1.46 - 1.57: 14989 1.57 - 1.69: 0 1.69 - 1.80: 175 Bond restraints: 27615 Sorted by residual: bond pdb=" CA ASP C 74 " pdb=" C ASP C 74 " ideal model delta sigma weight residual 1.523 1.496 0.028 1.34e-02 5.57e+03 4.21e+00 bond pdb=" CA ASP E 74 " pdb=" C ASP E 74 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.19e+00 bond pdb=" CA ASP F 74 " pdb=" C ASP F 74 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.07e+00 bond pdb=" CA ASP A 74 " pdb=" C ASP A 74 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.06e+00 bond pdb=" CA ASP B 74 " pdb=" C ASP B 74 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 3.98e+00 ... (remaining 27610 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 540 107.08 - 113.80: 16812 113.80 - 120.52: 10212 120.52 - 127.24: 9581 127.24 - 133.96: 116 Bond angle restraints: 37261 Sorted by residual: angle pdb=" N VAL D 267 " pdb=" CA VAL D 267 " pdb=" C VAL D 267 " ideal model delta sigma weight residual 112.12 108.88 3.24 8.40e-01 1.42e+00 1.49e+01 angle pdb=" N VAL A 267 " pdb=" CA VAL A 267 " pdb=" C VAL A 267 " ideal model delta sigma weight residual 112.12 108.90 3.22 8.40e-01 1.42e+00 1.47e+01 angle pdb=" N VAL C 267 " pdb=" CA VAL C 267 " pdb=" C VAL C 267 " ideal model delta sigma weight residual 112.12 108.91 3.21 8.40e-01 1.42e+00 1.46e+01 angle pdb=" N VAL E 267 " pdb=" CA VAL E 267 " pdb=" C VAL E 267 " ideal model delta sigma weight residual 112.12 108.93 3.19 8.40e-01 1.42e+00 1.44e+01 angle pdb=" N VAL G 267 " pdb=" CA VAL G 267 " pdb=" C VAL G 267 " ideal model delta sigma weight residual 112.12 108.94 3.18 8.40e-01 1.42e+00 1.44e+01 ... (remaining 37256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 15482 15.96 - 31.91: 1395 31.91 - 47.87: 224 47.87 - 63.82: 56 63.82 - 79.78: 56 Dihedral angle restraints: 17213 sinusoidal: 6797 harmonic: 10416 Sorted by residual: dihedral pdb=" CA THR G 205 " pdb=" C THR G 205 " pdb=" N SER G 206 " pdb=" CA SER G 206 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA THR B 205 " pdb=" C THR B 205 " pdb=" N SER B 206 " pdb=" CA SER B 206 " ideal model delta harmonic sigma weight residual -180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA THR E 205 " pdb=" C THR E 205 " pdb=" N SER E 206 " pdb=" CA SER E 206 " ideal model delta harmonic sigma weight residual 180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 17210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2642 0.029 - 0.057: 1149 0.057 - 0.086: 453 0.086 - 0.115: 279 0.115 - 0.144: 41 Chirality restraints: 4564 Sorted by residual: chirality pdb=" CA VAL B 324 " pdb=" N VAL B 324 " pdb=" C VAL B 324 " pdb=" CB VAL B 324 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL G 324 " pdb=" N VAL G 324 " pdb=" C VAL G 324 " pdb=" CB VAL G 324 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL F 324 " pdb=" N VAL F 324 " pdb=" C VAL F 324 " pdb=" CB VAL F 324 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 4561 not shown) Planarity restraints: 4802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 232 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 233 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 232 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO G 233 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 233 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 233 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 232 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO C 233 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " 0.027 5.00e-02 4.00e+02 ... (remaining 4799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3840 2.75 - 3.29: 29886 3.29 - 3.82: 45276 3.82 - 4.36: 52624 4.36 - 4.90: 90258 Nonbonded interactions: 221884 Sorted by model distance: nonbonded pdb=" OG1 THR G 138 " pdb=" OE1 GLU G 140 " model vdw 2.210 2.440 nonbonded pdb=" OG1 THR A 138 " pdb=" OE1 GLU A 140 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR C 138 " pdb=" OE1 GLU C 140 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR E 138 " pdb=" OE1 GLU E 140 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR B 138 " pdb=" OE1 GLU B 140 " model vdw 2.211 2.440 ... (remaining 221879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.080 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 69.700 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 0.031 27615 Z= 0.235 Angle : 0.619 5.318 37261 Z= 0.378 Chirality : 0.042 0.144 4564 Planarity : 0.004 0.048 4802 Dihedral : 13.410 79.775 10507 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.71 % Allowed : 4.01 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.12), residues: 3661 helix: -1.13 (0.10), residues: 1988 sheet: -1.43 (0.21), residues: 490 loop : -1.92 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 42 HIS 0.001 0.000 HIS B 314 PHE 0.008 0.001 PHE F 213 TYR 0.007 0.001 TYR D 64 ARG 0.002 0.000 ARG E 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 361 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8051 (ttp) cc_final: 0.7837 (ttp) REVERT: A 217 TYR cc_start: 0.8806 (m-80) cc_final: 0.8143 (m-80) REVERT: A 224 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8572 (ptmt) REVERT: A 236 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8729 (pt0) REVERT: A 251 ASP cc_start: 0.8442 (t0) cc_final: 0.7408 (t0) REVERT: A 371 LEU cc_start: 0.8941 (tp) cc_final: 0.8727 (tp) REVERT: B 42 TRP cc_start: 0.8077 (p90) cc_final: 0.7863 (p90) REVERT: B 191 MET cc_start: 0.8407 (ttp) cc_final: 0.7867 (ttp) REVERT: B 217 TYR cc_start: 0.8621 (m-80) cc_final: 0.8046 (m-80) REVERT: B 251 ASP cc_start: 0.8632 (t0) cc_final: 0.8223 (t0) REVERT: B 393 ASP cc_start: 0.8645 (t0) cc_final: 0.8422 (t0) REVERT: B 487 MET cc_start: 0.8507 (mmm) cc_final: 0.8291 (mmm) REVERT: C 59 ASP cc_start: 0.7457 (t0) cc_final: 0.7222 (m-30) REVERT: C 217 TYR cc_start: 0.8784 (m-80) cc_final: 0.8072 (m-80) REVERT: C 224 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8519 (ptmt) REVERT: C 251 ASP cc_start: 0.8616 (t0) cc_final: 0.8149 (t70) REVERT: C 333 LYS cc_start: 0.9227 (mtpt) cc_final: 0.8802 (tptt) REVERT: C 370 LYS cc_start: 0.9433 (mttt) cc_final: 0.9161 (mmmt) REVERT: C 371 LEU cc_start: 0.9050 (tp) cc_final: 0.8813 (tp) REVERT: C 393 ASP cc_start: 0.8630 (t0) cc_final: 0.8419 (t0) REVERT: D 217 TYR cc_start: 0.8716 (m-80) cc_final: 0.8002 (m-80) REVERT: D 236 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8585 (pt0) REVERT: D 251 ASP cc_start: 0.8640 (t0) cc_final: 0.8060 (t70) REVERT: D 284 LYS cc_start: 0.9436 (mttm) cc_final: 0.9232 (mppt) REVERT: D 487 MET cc_start: 0.8395 (mmm) cc_final: 0.8194 (mmm) REVERT: E 217 TYR cc_start: 0.8663 (m-80) cc_final: 0.7992 (m-80) REVERT: E 224 LYS cc_start: 0.8726 (ptpt) cc_final: 0.8507 (ptmt) REVERT: E 321 GLU cc_start: 0.8209 (mp0) cc_final: 0.8001 (mp0) REVERT: E 370 LYS cc_start: 0.9391 (mttt) cc_final: 0.9070 (mmmt) REVERT: E 371 LEU cc_start: 0.9026 (tp) cc_final: 0.8819 (tp) REVERT: F 217 TYR cc_start: 0.8730 (m-80) cc_final: 0.7910 (m-80) REVERT: F 224 LYS cc_start: 0.8687 (ptpt) cc_final: 0.8476 (ptmt) REVERT: F 251 ASP cc_start: 0.8591 (t0) cc_final: 0.7996 (t70) REVERT: F 284 LYS cc_start: 0.9442 (mttm) cc_final: 0.9240 (mppt) REVERT: G 42 TRP cc_start: 0.8198 (p90) cc_final: 0.7991 (p-90) REVERT: G 217 TYR cc_start: 0.8679 (m-80) cc_final: 0.7867 (m-80) REVERT: G 224 LYS cc_start: 0.8510 (ptpt) cc_final: 0.8296 (ptmt) REVERT: G 370 LYS cc_start: 0.9405 (mttt) cc_final: 0.9126 (mtpt) outliers start: 21 outliers final: 9 residues processed: 375 average time/residue: 0.4259 time to fit residues: 243.6204 Evaluate side-chains 249 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 324 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 330 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 204 ASN A 229 GLN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN B 132 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN C 132 GLN C 204 ASN C 229 GLN C 286 GLN C 340 GLN D 132 GLN D 204 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN E 132 GLN E 229 GLN E 286 GLN E 340 GLN F 132 GLN F 229 GLN F 340 GLN G 132 GLN G 229 GLN G 286 GLN G 340 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27615 Z= 0.175 Angle : 0.563 6.652 37261 Z= 0.296 Chirality : 0.043 0.187 4564 Planarity : 0.004 0.051 4802 Dihedral : 5.477 76.961 3848 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.89 % Allowed : 11.05 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3661 helix: 0.52 (0.12), residues: 1939 sheet: -0.69 (0.21), residues: 560 loop : -1.24 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 42 HIS 0.002 0.001 HIS C 314 PHE 0.013 0.001 PHE E 213 TYR 0.020 0.002 TYR C 477 ARG 0.006 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 279 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8588 (m-80) cc_final: 0.8022 (m-80) REVERT: A 224 LYS cc_start: 0.8898 (ptpt) cc_final: 0.8614 (ptmt) REVERT: A 251 ASP cc_start: 0.8547 (t0) cc_final: 0.7589 (t0) REVERT: A 371 LEU cc_start: 0.9008 (tp) cc_final: 0.8771 (tp) REVERT: B 217 TYR cc_start: 0.8441 (m-80) cc_final: 0.7907 (m-80) REVERT: B 393 ASP cc_start: 0.8607 (t0) cc_final: 0.8379 (t0) REVERT: C 50 ASP cc_start: 0.8003 (t0) cc_final: 0.7777 (t0) REVERT: C 191 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7726 (ttm) REVERT: C 217 TYR cc_start: 0.8662 (m-80) cc_final: 0.8048 (m-80) REVERT: C 224 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8523 (ptmt) REVERT: C 251 ASP cc_start: 0.8558 (t0) cc_final: 0.7888 (t70) REVERT: C 333 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8664 (tptt) REVERT: C 393 ASP cc_start: 0.8628 (t0) cc_final: 0.8401 (t0) REVERT: D 217 TYR cc_start: 0.8583 (m-80) cc_final: 0.7919 (m-80) REVERT: D 224 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8591 (ttmt) REVERT: D 284 LYS cc_start: 0.9377 (mttm) cc_final: 0.9174 (mppt) REVERT: D 487 MET cc_start: 0.8355 (mmm) cc_final: 0.7977 (mmt) REVERT: E 217 TYR cc_start: 0.8572 (m-80) cc_final: 0.7848 (m-80) REVERT: E 224 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8519 (ptmt) REVERT: E 251 ASP cc_start: 0.8616 (t0) cc_final: 0.7745 (t0) REVERT: E 290 MET cc_start: 0.9209 (mtp) cc_final: 0.9007 (mtm) REVERT: F 42 TRP cc_start: 0.8045 (p90) cc_final: 0.7825 (p-90) REVERT: F 217 TYR cc_start: 0.8685 (m-80) cc_final: 0.7927 (m-80) REVERT: F 224 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8473 (ptmt) REVERT: F 251 ASP cc_start: 0.8621 (t0) cc_final: 0.7754 (t0) REVERT: G 191 MET cc_start: 0.8032 (ttp) cc_final: 0.7657 (ttm) REVERT: G 217 TYR cc_start: 0.8482 (m-80) cc_final: 0.7639 (m-80) REVERT: G 224 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8369 (ptmt) REVERT: G 241 HIS cc_start: 0.7275 (m170) cc_final: 0.6666 (m90) REVERT: G 251 ASP cc_start: 0.8621 (t0) cc_final: 0.7644 (t0) REVERT: G 397 ASP cc_start: 0.8811 (t0) cc_final: 0.8572 (t0) outliers start: 56 outliers final: 21 residues processed: 315 average time/residue: 0.3534 time to fit residues: 181.2532 Evaluate side-chains 247 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 224 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 324 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 225 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 chunk 294 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN G 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27615 Z= 0.195 Angle : 0.576 10.471 37261 Z= 0.296 Chirality : 0.042 0.192 4564 Planarity : 0.004 0.055 4802 Dihedral : 4.706 32.713 3836 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.99 % Allowed : 13.92 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3661 helix: 1.02 (0.12), residues: 1939 sheet: -0.61 (0.21), residues: 574 loop : -1.27 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 42 HIS 0.000 0.000 HIS C 314 PHE 0.012 0.001 PHE B 213 TYR 0.020 0.001 TYR E 477 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8609 (m-80) cc_final: 0.7957 (m-80) REVERT: A 224 LYS cc_start: 0.8933 (ptpt) cc_final: 0.8634 (ptmt) REVERT: A 251 ASP cc_start: 0.8453 (t0) cc_final: 0.7507 (t0) REVERT: A 333 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8645 (tptt) REVERT: B 224 LYS cc_start: 0.8775 (ptpt) cc_final: 0.8506 (ptmt) REVERT: B 284 LYS cc_start: 0.9542 (mppt) cc_final: 0.9320 (mmmm) REVERT: B 393 ASP cc_start: 0.8622 (t0) cc_final: 0.8390 (t0) REVERT: C 50 ASP cc_start: 0.8006 (t0) cc_final: 0.7612 (t0) REVERT: C 217 TYR cc_start: 0.8599 (m-80) cc_final: 0.7967 (m-80) REVERT: C 224 LYS cc_start: 0.8824 (ptpt) cc_final: 0.8521 (ptmt) REVERT: C 241 HIS cc_start: 0.7240 (m170) cc_final: 0.6445 (m90) REVERT: C 251 ASP cc_start: 0.8509 (t0) cc_final: 0.7992 (t70) REVERT: C 333 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8647 (tptt) REVERT: C 393 ASP cc_start: 0.8632 (t0) cc_final: 0.8408 (t0) REVERT: D 217 TYR cc_start: 0.8594 (m-80) cc_final: 0.7902 (m-80) REVERT: D 241 HIS cc_start: 0.7380 (m170) cc_final: 0.6843 (m90) REVERT: D 251 ASP cc_start: 0.8474 (t0) cc_final: 0.8220 (t70) REVERT: D 284 LYS cc_start: 0.9370 (mttm) cc_final: 0.9158 (mppt) REVERT: D 487 MET cc_start: 0.8215 (mmm) cc_final: 0.7911 (mmm) REVERT: E 217 TYR cc_start: 0.8561 (m-80) cc_final: 0.7819 (m-80) REVERT: E 224 LYS cc_start: 0.8810 (ptpt) cc_final: 0.8540 (ptmt) REVERT: E 241 HIS cc_start: 0.7190 (m170) cc_final: 0.6450 (m90) REVERT: E 251 ASP cc_start: 0.8618 (t0) cc_final: 0.7794 (t0) REVERT: E 290 MET cc_start: 0.9344 (mtp) cc_final: 0.9075 (mtt) REVERT: F 217 TYR cc_start: 0.8618 (m-80) cc_final: 0.7842 (m-80) REVERT: F 224 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8451 (ptmt) REVERT: F 241 HIS cc_start: 0.7435 (m170) cc_final: 0.6704 (m90) REVERT: F 251 ASP cc_start: 0.8619 (t0) cc_final: 0.7626 (t0) REVERT: G 217 TYR cc_start: 0.8472 (m-80) cc_final: 0.7632 (m-80) REVERT: G 224 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8397 (ptmt) REVERT: G 241 HIS cc_start: 0.7286 (m170) cc_final: 0.6600 (m90) REVERT: G 251 ASP cc_start: 0.8555 (t0) cc_final: 0.7548 (t0) REVERT: G 397 ASP cc_start: 0.8859 (t0) cc_final: 0.8585 (t0) outliers start: 59 outliers final: 41 residues processed: 311 average time/residue: 0.3458 time to fit residues: 178.8072 Evaluate side-chains 282 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 241 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 332 optimal weight: 10.0000 chunk 351 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN E 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27615 Z= 0.185 Angle : 0.566 12.666 37261 Z= 0.287 Chirality : 0.042 0.212 4564 Planarity : 0.004 0.056 4802 Dihedral : 4.522 31.146 3836 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.53 % Allowed : 14.66 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3661 helix: 1.29 (0.12), residues: 1939 sheet: -0.49 (0.21), residues: 574 loop : -1.29 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 42 HIS 0.001 0.000 HIS B 314 PHE 0.013 0.001 PHE F 213 TYR 0.027 0.002 TYR G 64 ARG 0.002 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 268 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8557 (m-80) cc_final: 0.7901 (m-80) REVERT: A 224 LYS cc_start: 0.8945 (ptpt) cc_final: 0.8635 (ptmt) REVERT: A 251 ASP cc_start: 0.8437 (t0) cc_final: 0.7535 (t0) REVERT: A 333 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8641 (tptt) REVERT: A 459 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8610 (t) REVERT: B 224 LYS cc_start: 0.8811 (ptpt) cc_final: 0.8535 (ptmt) REVERT: B 393 ASP cc_start: 0.8649 (t0) cc_final: 0.8412 (t0) REVERT: C 217 TYR cc_start: 0.8599 (m-80) cc_final: 0.8010 (m-80) REVERT: C 224 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8525 (ptmt) REVERT: C 236 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: C 241 HIS cc_start: 0.7435 (m170) cc_final: 0.6657 (m90) REVERT: C 251 ASP cc_start: 0.8489 (t0) cc_final: 0.7862 (t70) REVERT: C 333 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8628 (tptt) REVERT: C 393 ASP cc_start: 0.8629 (t0) cc_final: 0.8396 (t0) REVERT: D 217 TYR cc_start: 0.8593 (m-80) cc_final: 0.7936 (m-80) REVERT: D 241 HIS cc_start: 0.7430 (m170) cc_final: 0.6822 (m90) REVERT: D 251 ASP cc_start: 0.8428 (t0) cc_final: 0.8112 (t0) REVERT: D 284 LYS cc_start: 0.9364 (mttm) cc_final: 0.9154 (mppt) REVERT: D 487 MET cc_start: 0.8161 (mmm) cc_final: 0.7805 (mmm) REVERT: E 217 TYR cc_start: 0.8530 (m-80) cc_final: 0.7728 (m-80) REVERT: E 224 LYS cc_start: 0.8796 (ptpt) cc_final: 0.8556 (ptmt) REVERT: E 251 ASP cc_start: 0.8659 (t0) cc_final: 0.7858 (t0) REVERT: E 290 MET cc_start: 0.9325 (mtp) cc_final: 0.9065 (mmm) REVERT: F 191 MET cc_start: 0.7629 (mtt) cc_final: 0.6664 (ttm) REVERT: F 217 TYR cc_start: 0.8590 (m-80) cc_final: 0.7823 (m-80) REVERT: F 224 LYS cc_start: 0.8722 (ptpt) cc_final: 0.8458 (ptmt) REVERT: F 251 ASP cc_start: 0.8526 (t0) cc_final: 0.7460 (t0) REVERT: G 224 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8424 (ptmt) REVERT: G 251 ASP cc_start: 0.8535 (t0) cc_final: 0.7541 (t0) REVERT: G 397 ASP cc_start: 0.8860 (t0) cc_final: 0.8623 (t0) REVERT: G 459 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8660 (t) REVERT: G 487 MET cc_start: 0.7819 (mmm) cc_final: 0.7356 (mmm) outliers start: 75 outliers final: 50 residues processed: 326 average time/residue: 0.3328 time to fit residues: 182.8090 Evaluate side-chains 290 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 7.9990 chunk 199 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 300 optimal weight: 0.3980 chunk 243 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS G 40 GLN G 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27615 Z= 0.147 Angle : 0.549 8.323 37261 Z= 0.278 Chirality : 0.041 0.224 4564 Planarity : 0.004 0.058 4802 Dihedral : 4.367 29.370 3836 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.99 % Allowed : 16.11 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3661 helix: 1.43 (0.12), residues: 1974 sheet: -0.36 (0.21), residues: 574 loop : -1.06 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP G 42 HIS 0.002 0.000 HIS B 314 PHE 0.015 0.001 PHE A 213 TYR 0.025 0.001 TYR A 477 ARG 0.003 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 263 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9282 (mm) REVERT: A 217 TYR cc_start: 0.8500 (m-80) cc_final: 0.7841 (m-80) REVERT: A 224 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8662 (ptmt) REVERT: A 251 ASP cc_start: 0.8385 (t0) cc_final: 0.7610 (t0) REVERT: A 253 ASP cc_start: 0.9240 (t70) cc_final: 0.8821 (t0) REVERT: A 333 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8539 (tptt) REVERT: A 487 MET cc_start: 0.8352 (mmt) cc_final: 0.7626 (mmm) REVERT: B 224 LYS cc_start: 0.8847 (ptpt) cc_final: 0.8583 (ptmt) REVERT: B 393 ASP cc_start: 0.8646 (t0) cc_final: 0.8403 (t0) REVERT: C 217 TYR cc_start: 0.8449 (m-80) cc_final: 0.7850 (m-80) REVERT: C 224 LYS cc_start: 0.8836 (ptpt) cc_final: 0.8526 (ptmt) REVERT: C 241 HIS cc_start: 0.7485 (m170) cc_final: 0.6708 (m90) REVERT: C 251 ASP cc_start: 0.8387 (t0) cc_final: 0.7743 (t70) REVERT: C 333 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8605 (tptt) REVERT: C 393 ASP cc_start: 0.8618 (t0) cc_final: 0.8380 (t0) REVERT: D 217 TYR cc_start: 0.8478 (m-80) cc_final: 0.7843 (m-80) REVERT: D 241 HIS cc_start: 0.7439 (m170) cc_final: 0.6822 (m90) REVERT: D 251 ASP cc_start: 0.8346 (t0) cc_final: 0.8010 (t0) REVERT: D 284 LYS cc_start: 0.9358 (mttm) cc_final: 0.9147 (mppt) REVERT: E 217 TYR cc_start: 0.8514 (m-80) cc_final: 0.7812 (m-80) REVERT: E 224 LYS cc_start: 0.8825 (ptpt) cc_final: 0.8575 (ptmt) REVERT: E 251 ASP cc_start: 0.8595 (t0) cc_final: 0.7720 (t0) REVERT: E 487 MET cc_start: 0.7869 (mmt) cc_final: 0.7539 (mmm) REVERT: F 217 TYR cc_start: 0.8530 (m-80) cc_final: 0.7816 (m-80) REVERT: F 224 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8518 (ptmt) REVERT: F 251 ASP cc_start: 0.8430 (t0) cc_final: 0.7315 (t0) REVERT: G 217 TYR cc_start: 0.8521 (m-80) cc_final: 0.7798 (m-80) REVERT: G 224 LYS cc_start: 0.8727 (ptpt) cc_final: 0.8448 (ptmt) REVERT: G 251 ASP cc_start: 0.8606 (t0) cc_final: 0.7672 (t0) REVERT: G 397 ASP cc_start: 0.8843 (t0) cc_final: 0.8599 (t0) REVERT: G 459 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8631 (t) outliers start: 59 outliers final: 44 residues processed: 308 average time/residue: 0.3431 time to fit residues: 176.5509 Evaluate side-chains 281 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 1.9990 chunk 316 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 206 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 352 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27615 Z= 0.186 Angle : 0.574 14.121 37261 Z= 0.288 Chirality : 0.042 0.203 4564 Planarity : 0.004 0.058 4802 Dihedral : 4.309 28.519 3836 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.32 % Allowed : 16.98 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3661 helix: 1.48 (0.12), residues: 1974 sheet: -0.30 (0.21), residues: 574 loop : -1.01 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP D 42 HIS 0.001 0.000 HIS B 314 PHE 0.009 0.001 PHE G 193 TYR 0.020 0.001 TYR E 477 ARG 0.002 0.000 ARG G 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 245 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9300 (mm) REVERT: A 224 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8620 (ptmt) REVERT: A 251 ASP cc_start: 0.8408 (t0) cc_final: 0.6316 (t0) REVERT: A 253 ASP cc_start: 0.9275 (t70) cc_final: 0.8951 (m-30) REVERT: A 333 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8521 (tptt) REVERT: A 522 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: B 224 LYS cc_start: 0.8812 (ptpt) cc_final: 0.8542 (ptmt) REVERT: B 393 ASP cc_start: 0.8665 (t0) cc_final: 0.8425 (t0) REVERT: C 217 TYR cc_start: 0.8452 (m-80) cc_final: 0.7807 (m-80) REVERT: C 224 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8593 (ptmt) REVERT: C 251 ASP cc_start: 0.8455 (t0) cc_final: 0.8088 (t70) REVERT: C 253 ASP cc_start: 0.9268 (t70) cc_final: 0.8879 (t0) REVERT: C 333 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8598 (tptt) REVERT: C 393 ASP cc_start: 0.8630 (t0) cc_final: 0.8398 (t0) REVERT: D 251 ASP cc_start: 0.8294 (t0) cc_final: 0.7956 (t0) REVERT: D 284 LYS cc_start: 0.9363 (mttm) cc_final: 0.9148 (mppt) REVERT: D 487 MET cc_start: 0.8340 (mmt) cc_final: 0.7966 (mmt) REVERT: E 217 TYR cc_start: 0.8548 (m-80) cc_final: 0.7866 (m-80) REVERT: E 224 LYS cc_start: 0.8814 (ptpt) cc_final: 0.8560 (ptmt) REVERT: E 251 ASP cc_start: 0.8582 (t0) cc_final: 0.7720 (t0) REVERT: F 217 TYR cc_start: 0.8517 (m-80) cc_final: 0.7812 (m-80) REVERT: F 224 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8520 (ptmt) REVERT: F 251 ASP cc_start: 0.8491 (t0) cc_final: 0.7364 (t0) REVERT: F 253 ASP cc_start: 0.9191 (t70) cc_final: 0.8830 (t0) REVERT: G 224 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8447 (ptmt) REVERT: G 251 ASP cc_start: 0.8560 (t0) cc_final: 0.7645 (t0) REVERT: G 397 ASP cc_start: 0.8852 (t0) cc_final: 0.8611 (t0) REVERT: G 459 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8643 (t) outliers start: 69 outliers final: 53 residues processed: 298 average time/residue: 0.3458 time to fit residues: 172.4890 Evaluate side-chains 287 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 231 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 200 optimal weight: 0.1980 chunk 257 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 350 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27615 Z= 0.188 Angle : 0.575 12.196 37261 Z= 0.289 Chirality : 0.042 0.227 4564 Planarity : 0.004 0.060 4802 Dihedral : 4.289 28.093 3836 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.49 % Allowed : 17.32 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3661 helix: 1.55 (0.12), residues: 1974 sheet: -0.38 (0.21), residues: 588 loop : -1.11 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP D 42 HIS 0.001 0.000 HIS B 314 PHE 0.015 0.001 PHE A 213 TYR 0.021 0.001 TYR D 64 ARG 0.003 0.000 ARG G 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 243 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9294 (mm) REVERT: A 224 LYS cc_start: 0.8926 (ptpt) cc_final: 0.8629 (ptmt) REVERT: A 251 ASP cc_start: 0.8393 (t0) cc_final: 0.6229 (t0) REVERT: A 253 ASP cc_start: 0.9282 (t70) cc_final: 0.8945 (m-30) REVERT: A 333 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8519 (tptt) REVERT: A 522 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 42 TRP cc_start: 0.7968 (p-90) cc_final: 0.7545 (p-90) REVERT: B 224 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8510 (ptmt) REVERT: B 262 LEU cc_start: 0.9523 (tp) cc_final: 0.9318 (pp) REVERT: B 393 ASP cc_start: 0.8646 (t0) cc_final: 0.8401 (t0) REVERT: C 217 TYR cc_start: 0.8447 (m-80) cc_final: 0.7823 (m-80) REVERT: C 224 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8601 (ptmt) REVERT: C 251 ASP cc_start: 0.8417 (t0) cc_final: 0.8026 (t70) REVERT: C 253 ASP cc_start: 0.9280 (t70) cc_final: 0.8872 (t0) REVERT: C 333 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8590 (tptt) REVERT: C 393 ASP cc_start: 0.8630 (t0) cc_final: 0.8396 (t0) REVERT: D 251 ASP cc_start: 0.8395 (t0) cc_final: 0.7018 (t0) REVERT: D 253 ASP cc_start: 0.9230 (t70) cc_final: 0.8842 (m-30) REVERT: D 284 LYS cc_start: 0.9361 (mttm) cc_final: 0.9148 (mppt) REVERT: D 487 MET cc_start: 0.8327 (mmt) cc_final: 0.7995 (mmt) REVERT: E 191 MET cc_start: 0.7835 (mmt) cc_final: 0.7604 (tpp) REVERT: E 217 TYR cc_start: 0.8604 (m-80) cc_final: 0.7904 (m-80) REVERT: E 224 LYS cc_start: 0.8821 (ptpt) cc_final: 0.8567 (ptmt) REVERT: E 251 ASP cc_start: 0.8529 (t0) cc_final: 0.7725 (t0) REVERT: F 224 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8524 (ptmt) REVERT: F 251 ASP cc_start: 0.8460 (t0) cc_final: 0.7615 (t0) REVERT: F 253 ASP cc_start: 0.9218 (t70) cc_final: 0.8878 (t0) REVERT: G 174 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8559 (p) REVERT: G 224 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8441 (ptmt) REVERT: G 251 ASP cc_start: 0.8556 (t0) cc_final: 0.6266 (t0) REVERT: G 253 ASP cc_start: 0.9263 (t70) cc_final: 0.8920 (m-30) REVERT: G 397 ASP cc_start: 0.8868 (t0) cc_final: 0.8624 (t0) outliers start: 74 outliers final: 57 residues processed: 301 average time/residue: 0.3355 time to fit residues: 169.8168 Evaluate side-chains 293 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 233 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 239 optimal weight: 0.3980 chunk 173 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27615 Z= 0.144 Angle : 0.576 15.358 37261 Z= 0.285 Chirality : 0.042 0.237 4564 Planarity : 0.004 0.063 4802 Dihedral : 4.146 27.331 3836 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.16 % Allowed : 17.89 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3661 helix: 1.78 (0.12), residues: 1960 sheet: -0.34 (0.21), residues: 602 loop : -1.42 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP G 42 HIS 0.001 0.000 HIS B 314 PHE 0.008 0.001 PHE A 213 TYR 0.022 0.001 TYR A 477 ARG 0.002 0.000 ARG G 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9270 (mm) REVERT: A 224 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8630 (ptmt) REVERT: A 251 ASP cc_start: 0.8376 (t0) cc_final: 0.6553 (t0) REVERT: A 253 ASP cc_start: 0.9306 (t70) cc_final: 0.8991 (m-30) REVERT: A 333 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8595 (tptt) REVERT: B 42 TRP cc_start: 0.7961 (p-90) cc_final: 0.7538 (p-90) REVERT: B 224 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8504 (ptmt) REVERT: B 393 ASP cc_start: 0.8624 (t0) cc_final: 0.8398 (t0) REVERT: C 217 TYR cc_start: 0.8362 (m-80) cc_final: 0.7781 (m-80) REVERT: C 224 LYS cc_start: 0.8867 (ptpt) cc_final: 0.8583 (ptmt) REVERT: C 251 ASP cc_start: 0.8328 (t0) cc_final: 0.6783 (t0) REVERT: C 393 ASP cc_start: 0.8620 (t0) cc_final: 0.8385 (t0) REVERT: D 251 ASP cc_start: 0.8377 (t0) cc_final: 0.7103 (t0) REVERT: D 253 ASP cc_start: 0.9293 (t70) cc_final: 0.8958 (m-30) REVERT: D 487 MET cc_start: 0.8357 (mmt) cc_final: 0.8069 (mmt) REVERT: E 42 TRP cc_start: 0.7875 (p-90) cc_final: 0.7536 (p-90) REVERT: E 217 TYR cc_start: 0.8528 (m-80) cc_final: 0.7834 (m-80) REVERT: E 224 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8634 (ptmt) REVERT: E 251 ASP cc_start: 0.8526 (t0) cc_final: 0.7964 (t0) REVERT: E 262 LEU cc_start: 0.9516 (tp) cc_final: 0.9286 (pp) REVERT: F 224 LYS cc_start: 0.8818 (ptpt) cc_final: 0.8498 (ptmt) REVERT: F 251 ASP cc_start: 0.8454 (t0) cc_final: 0.6317 (t0) REVERT: F 253 ASP cc_start: 0.9255 (t70) cc_final: 0.9000 (m-30) REVERT: F 314 HIS cc_start: 0.8488 (t70) cc_final: 0.8268 (p90) REVERT: G 174 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8530 (p) REVERT: G 224 LYS cc_start: 0.8734 (ptpt) cc_final: 0.8437 (ptmt) REVERT: G 251 ASP cc_start: 0.8487 (t0) cc_final: 0.7345 (t0) REVERT: G 253 ASP cc_start: 0.9244 (t70) cc_final: 0.9012 (p0) REVERT: G 397 ASP cc_start: 0.8869 (t0) cc_final: 0.8619 (t0) outliers start: 64 outliers final: 49 residues processed: 299 average time/residue: 0.3386 time to fit residues: 169.0985 Evaluate side-chains 285 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 234 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 309 optimal weight: 8.9990 chunk 325 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 229 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN E 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27615 Z= 0.283 Angle : 0.626 14.659 37261 Z= 0.315 Chirality : 0.043 0.316 4564 Planarity : 0.004 0.062 4802 Dihedral : 4.300 28.315 3836 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.95 % Allowed : 18.77 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3661 helix: 1.61 (0.12), residues: 1988 sheet: -0.26 (0.21), residues: 588 loop : -1.12 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP G 42 HIS 0.001 0.000 HIS B 314 PHE 0.022 0.001 PHE B 213 TYR 0.021 0.001 TYR D 64 ARG 0.002 0.000 ARG G 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 234 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9333 (mm) REVERT: A 224 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8629 (ptmt) REVERT: A 251 ASP cc_start: 0.8399 (t0) cc_final: 0.6513 (t0) REVERT: A 253 ASP cc_start: 0.9352 (t70) cc_final: 0.8968 (m-30) REVERT: A 333 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8609 (tptt) REVERT: B 224 LYS cc_start: 0.8769 (ptpt) cc_final: 0.8479 (ptmt) REVERT: B 253 ASP cc_start: 0.9295 (t70) cc_final: 0.8994 (t70) REVERT: B 393 ASP cc_start: 0.8641 (t0) cc_final: 0.8415 (t0) REVERT: C 224 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8580 (ptmt) REVERT: C 393 ASP cc_start: 0.8618 (t0) cc_final: 0.8386 (t0) REVERT: D 251 ASP cc_start: 0.8382 (t0) cc_final: 0.8045 (t0) REVERT: D 262 LEU cc_start: 0.9505 (tp) cc_final: 0.9266 (pp) REVERT: D 487 MET cc_start: 0.8379 (mmt) cc_final: 0.8081 (mmt) REVERT: E 224 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8620 (ptmt) REVERT: E 251 ASP cc_start: 0.8564 (t0) cc_final: 0.7748 (t0) REVERT: E 262 LEU cc_start: 0.9516 (tp) cc_final: 0.9286 (pp) REVERT: F 224 LYS cc_start: 0.8810 (ptpt) cc_final: 0.8510 (ptmt) REVERT: F 251 ASP cc_start: 0.8463 (t0) cc_final: 0.6472 (t0) REVERT: F 253 ASP cc_start: 0.9287 (t70) cc_final: 0.9043 (m-30) REVERT: F 314 HIS cc_start: 0.8470 (t70) cc_final: 0.8212 (p90) REVERT: G 224 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8396 (ptmt) REVERT: G 251 ASP cc_start: 0.8472 (t0) cc_final: 0.7371 (t0) REVERT: G 253 ASP cc_start: 0.9269 (t70) cc_final: 0.8985 (p0) REVERT: G 290 MET cc_start: 0.9298 (mtm) cc_final: 0.9091 (ptp) REVERT: G 397 ASP cc_start: 0.8887 (t0) cc_final: 0.8636 (t0) outliers start: 58 outliers final: 49 residues processed: 276 average time/residue: 0.3444 time to fit residues: 159.0502 Evaluate side-chains 278 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 1.9990 chunk 345 optimal weight: 30.0000 chunk 211 optimal weight: 0.7980 chunk 164 optimal weight: 0.0870 chunk 240 optimal weight: 5.9990 chunk 362 optimal weight: 2.9990 chunk 333 optimal weight: 0.1980 chunk 288 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27615 Z= 0.161 Angle : 0.605 12.222 37261 Z= 0.296 Chirality : 0.042 0.331 4564 Planarity : 0.004 0.065 4802 Dihedral : 4.150 27.768 3836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.65 % Allowed : 19.04 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3661 helix: 1.89 (0.12), residues: 1960 sheet: -0.27 (0.21), residues: 602 loop : -1.45 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP G 42 HIS 0.001 0.000 HIS B 314 PHE 0.015 0.001 PHE B 213 TYR 0.023 0.002 TYR A 477 ARG 0.004 0.000 ARG G 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9588 (OUTLIER) cc_final: 0.9303 (mm) REVERT: A 224 LYS cc_start: 0.8849 (ptpt) cc_final: 0.8570 (ptmt) REVERT: A 251 ASP cc_start: 0.8387 (t0) cc_final: 0.6609 (t0) REVERT: A 253 ASP cc_start: 0.9391 (t70) cc_final: 0.9028 (m-30) REVERT: A 314 HIS cc_start: 0.8395 (t70) cc_final: 0.8185 (p90) REVERT: A 333 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8545 (tptt) REVERT: B 224 LYS cc_start: 0.8719 (ptpt) cc_final: 0.8423 (ptmt) REVERT: B 253 ASP cc_start: 0.9264 (t70) cc_final: 0.8975 (t70) REVERT: B 393 ASP cc_start: 0.8607 (t0) cc_final: 0.8389 (t0) REVERT: C 217 TYR cc_start: 0.8409 (m-80) cc_final: 0.7782 (m-80) REVERT: C 224 LYS cc_start: 0.8769 (ptpt) cc_final: 0.8444 (ptmt) REVERT: C 393 ASP cc_start: 0.8616 (t0) cc_final: 0.8382 (t0) REVERT: D 251 ASP cc_start: 0.8317 (t0) cc_final: 0.7845 (t0) REVERT: D 253 ASP cc_start: 0.9340 (t70) cc_final: 0.9047 (p0) REVERT: D 262 LEU cc_start: 0.9508 (tp) cc_final: 0.9260 (pp) REVERT: D 487 MET cc_start: 0.8363 (mmt) cc_final: 0.8118 (mmt) REVERT: E 42 TRP cc_start: 0.7879 (p-90) cc_final: 0.7588 (p-90) REVERT: E 224 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8664 (ptmt) REVERT: E 251 ASP cc_start: 0.8530 (t0) cc_final: 0.7967 (t0) REVERT: E 262 LEU cc_start: 0.9500 (tp) cc_final: 0.9276 (pp) REVERT: F 224 LYS cc_start: 0.8820 (ptpt) cc_final: 0.8530 (ptmt) REVERT: F 251 ASP cc_start: 0.8391 (t0) cc_final: 0.6378 (t0) REVERT: F 253 ASP cc_start: 0.9281 (t70) cc_final: 0.9015 (m-30) REVERT: F 314 HIS cc_start: 0.8447 (t70) cc_final: 0.8200 (p90) REVERT: G 224 LYS cc_start: 0.8676 (ptpt) cc_final: 0.8370 (ptmt) REVERT: G 251 ASP cc_start: 0.8443 (t0) cc_final: 0.7333 (t0) REVERT: G 397 ASP cc_start: 0.8876 (t0) cc_final: 0.8624 (t0) outliers start: 49 outliers final: 46 residues processed: 272 average time/residue: 0.3372 time to fit residues: 154.6398 Evaluate side-chains 274 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 227 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 520 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.102294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.062143 restraints weight = 69434.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065965 restraints weight = 37647.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066320 restraints weight = 22334.202| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 27615 Z= 0.417 Angle : 0.697 13.726 37261 Z= 0.356 Chirality : 0.045 0.313 4564 Planarity : 0.004 0.062 4802 Dihedral : 4.557 29.075 3836 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.75 % Allowed : 19.47 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3661 helix: 1.45 (0.12), residues: 1960 sheet: -0.28 (0.21), residues: 574 loop : -1.29 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP C 42 HIS 0.001 0.001 HIS B 314 PHE 0.016 0.002 PHE A 213 TYR 0.027 0.002 TYR C 64 ARG 0.003 0.000 ARG B 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4533.35 seconds wall clock time: 85 minutes 9.28 seconds (5109.28 seconds total)