Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 06:43:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/04_2023/7azp_11950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/04_2023/7azp_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_11950/04_2023/7azp_11950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/04_2023/7azp_11950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/04_2023/7azp_11950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7azp_11950/04_2023/7azp_11950.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 14.24, per 1000 atoms: 0.52 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: 11.76 Conformation dependent library (CDL) restraints added in 4.8 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: 2.13 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: 11.36 Time building geometry restraints manager: 12.57 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: 0.760 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: 6.280 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 71.900 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.010 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.715 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 outliers start: 21 outliers final: 9 residues processed: 375 average time/residue: 0.4375 time to fit residues: 252.1335 Evaluate side-chains 225 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 3.420 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2501 time to fit residues: 8.7243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 330 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN B 132 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN C 132 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 340 GLN D 132 GLN D 204 ASN D 229 GLN ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN E 132 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN E 340 GLN F 132 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN F 340 GLN G 132 GLN G 229 GLN G 340 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 27615 Z= 0.201 Angle : 0.578 6.640 37261 Z= 0.305 Chirality : 0.043 0.189 4564 Planarity : 0.004 0.049 4802 Dihedral : 4.750 24.094 3829 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 2.12 % 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: 0.42 (0.12), residues: 1953 sheet: -0.74 (0.21), residues: 560 loop : -1.40 (0.18), residues: 1148 *********************** 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 327 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 264 time to evaluate : 3.541 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 outliers start: 63 outliers final: 21 residues processed: 292 average time/residue: 0.3683 time to fit residues: 177.3294 Evaluate side-chains 233 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 3.434 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2832 time to fit residues: 15.1771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 275 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 357 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 27615 Z= 0.171 Angle : 0.585 10.920 37261 Z= 0.299 Chirality : 0.042 0.204 4564 Planarity : 0.004 0.056 4802 Dihedral : 4.586 23.524 3829 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.55 % 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: 0.02 (0.14), residues: 3661 helix: 1.04 (0.12), residues: 1953 sheet: -0.63 (0.21), residues: 574 loop : -1.36 (0.18), residues: 1134 *********************** 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 301 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 289 average time/residue: 0.3466 time to fit residues: 168.7177 Evaluate side-chains 237 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 3.393 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2447 time to fit residues: 16.1454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 0.9990 chunk 248 optimal weight: 0.0040 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 332 optimal weight: 9.9990 chunk 351 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 G 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 27615 Z= 0.169 Angle : 0.571 12.444 37261 Z= 0.290 Chirality : 0.042 0.210 4564 Planarity : 0.004 0.058 4802 Dihedral : 4.445 23.098 3829 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.92 % 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: 0.22 (0.14), residues: 3661 helix: 1.27 (0.12), residues: 1953 sheet: -0.58 (0.21), residues: 574 loop : -1.38 (0.18), residues: 1134 *********************** 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 298 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 32 residues processed: 283 average time/residue: 0.3312 time to fit residues: 161.3439 Evaluate side-chains 252 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 3.623 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2583 time to fit residues: 20.2889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 5 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 300 optimal weight: 0.6980 chunk 243 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 315 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 27615 Z= 0.149 Angle : 0.553 9.675 37261 Z= 0.282 Chirality : 0.041 0.214 4564 Planarity : 0.004 0.066 4802 Dihedral : 4.312 22.639 3829 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3661 helix: 1.45 (0.12), residues: 1960 sheet: -0.63 (0.20), residues: 616 loop : -1.28 (0.18), residues: 1085 *********************** 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 271 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 265 average time/residue: 0.3424 time to fit residues: 154.4070 Evaluate side-chains 229 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 3.462 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2504 time to fit residues: 11.7547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 206 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 352 optimal weight: 0.2980 chunk 292 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN E 214 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: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 27615 Z= 0.168 Angle : 0.573 13.502 37261 Z= 0.289 Chirality : 0.042 0.209 4564 Planarity : 0.004 0.064 4802 Dihedral : 4.261 21.964 3829 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.71 % 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: 0.56 (0.14), residues: 3661 helix: 1.56 (0.12), residues: 1960 sheet: -0.53 (0.20), residues: 616 loop : -1.24 (0.18), residues: 1085 *********************** 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 253 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 246 average time/residue: 0.3431 time to fit residues: 144.4814 Evaluate side-chains 219 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 3.633 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2477 time to fit residues: 9.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 296 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2973 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= 0.164 Angle : 0.573 11.756 37261 Z= 0.290 Chirality : 0.042 0.233 4564 Planarity : 0.004 0.065 4802 Dihedral : 4.200 21.788 3829 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3661 helix: 1.67 (0.12), residues: 1960 sheet: -0.40 (0.20), residues: 616 loop : -1.23 (0.18), residues: 1085 *********************** 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 238 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 235 average time/residue: 0.3500 time to fit residues: 139.7995 Evaluate side-chains 219 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2461 time to fit residues: 9.3811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 27615 Z= 0.187 Angle : 0.597 14.830 37261 Z= 0.298 Chirality : 0.042 0.184 4564 Planarity : 0.004 0.065 4802 Dihedral : 4.177 21.380 3829 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.34 % 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: 0.74 (0.14), residues: 3661 helix: 1.72 (0.12), residues: 1960 sheet: -0.33 (0.20), residues: 616 loop : -1.27 (0.18), residues: 1085 *********************** 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 226 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 222 average time/residue: 0.3560 time to fit residues: 135.3167 Evaluate side-chains 212 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 205 time to evaluate : 3.534 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2433 time to fit residues: 7.9756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 326 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 325 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 27615 Z= 0.175 Angle : 0.588 12.400 37261 Z= 0.294 Chirality : 0.042 0.297 4564 Planarity : 0.004 0.065 4802 Dihedral : 4.115 21.422 3829 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.37 % 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: 0.83 (0.14), residues: 3661 helix: 1.81 (0.12), residues: 1960 sheet: -0.30 (0.21), residues: 616 loop : -1.27 (0.18), residues: 1085 *********************** 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 223 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 221 average time/residue: 0.3684 time to fit residues: 137.0540 Evaluate side-chains 206 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 3.327 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2400 time to fit residues: 5.4485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 362 optimal weight: 0.7980 chunk 333 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3299 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= 0.160 Angle : 0.609 14.673 37261 Z= 0.298 Chirality : 0.041 0.270 4564 Planarity : 0.004 0.067 4802 Dihedral : 4.048 20.870 3829 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.34 % 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: 0.93 (0.14), residues: 3661 helix: 1.89 (0.12), residues: 1960 sheet: -0.20 (0.21), residues: 616 loop : -1.24 (0.18), residues: 1085 ********************** 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 222 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 218 average time/residue: 0.3631 time to fit residues: 134.1149 Evaluate side-chains 205 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 3.696 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2474 time to fit residues: 6.6203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.063041 restraints weight = 71886.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066146 restraints weight = 37873.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067282 restraints weight = 23244.972| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 27615 Z= 0.458 Angle : 0.717 13.676 37261 Z= 0.367 Chirality : 0.046 0.293 4564 Planarity : 0.004 0.063 4802 Dihedral : 4.532 22.072 3829 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.54 % 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: 0.48 (0.14), residues: 3661 helix: 1.44 (0.12), residues: 1960 sheet: -0.37 (0.21), residues: 616 loop : -1.28 (0.18), residues: 1085 =============================================================================== Job complete usr+sys time: 4222.73 seconds wall clock time: 79 minutes 22.25 seconds (4762.25 seconds total)