Starting phenix.real_space_refine on Thu Feb 5 20:48:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3v_62791/02_2026/9l3v_62791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3v_62791/02_2026/9l3v_62791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l3v_62791/02_2026/9l3v_62791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3v_62791/02_2026/9l3v_62791.map" model { file = "/net/cci-nas-00/data/ceres_data/9l3v_62791/02_2026/9l3v_62791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3v_62791/02_2026/9l3v_62791.cif" } resolution = 2.53 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 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= 0.049 sd= 0.782 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 129 5.16 5 C 12537 2.51 5 N 3390 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19743 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 28, 'TRANS': 389} Chain: "C" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 28, 'TRANS': 389} Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 28, 'TRANS': 389} Time building chain proxies: 3.99, per 1000 atoms: 0.20 Number of scatterers: 19743 At special positions: 0 Unit cell: (163.2, 150, 169.2, 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 129 16.00 O 3687 8.00 N 3390 7.00 C 12537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 29 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.02 Simple disulfide: pdb=" SG CYS D 20 " - pdb=" SG CYS D 128 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 29 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 270 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 207 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.02 Simple disulfide: pdb=" SG CYS F 20 " - pdb=" SG CYS F 128 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 29 " distance=2.03 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 270 " distance=2.03 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 207 " - pdb=" SG CYS F 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.65 Conformation dependent library (CDL) restraints added in 887.7 milliseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4794 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 64 sheets defined 15.1% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.378A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.153A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.631A pdb=" N PHE A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.657A pdb=" N VAL A 402 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 439 removed outlier: 4.236A pdb=" N ILE A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 367 through 375 removed outlier: 3.620A pdb=" N THR B 371 " --> pdb=" O HIS B 367 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 402 removed outlier: 3.771A pdb=" N THR B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 removed outlier: 4.086A pdb=" N VAL B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.389A pdb=" N THR C 115 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.114A pdb=" N GLY C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.620A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.690A pdb=" N VAL C 402 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 439 removed outlier: 4.251A pdb=" N ILE C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.589A pdb=" N THR D 371 " --> pdb=" O HIS D 367 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 372 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 402 removed outlier: 3.770A pdb=" N THR D 386 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER D 388 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 4.086A pdb=" N VAL D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.391A pdb=" N THR E 115 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 255 through 259 removed outlier: 4.214A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 3.607A pdb=" N PHE E 287 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.643A pdb=" N VAL E 402 " --> pdb=" O GLN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 439 removed outlier: 4.256A pdb=" N ILE E 435 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 226 through 228 No H-bonds generated for 'chain 'F' and resid 226 through 228' Processing helix chain 'F' and resid 355 through 366 Processing helix chain 'F' and resid 367 through 375 removed outlier: 3.596A pdb=" N THR F 371 " --> pdb=" O HIS F 367 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 372 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 402 removed outlier: 3.770A pdb=" N THR F 386 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 387 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER F 389 " --> pdb=" O GLY F 385 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS F 400 " --> pdb=" O ALA F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 421 removed outlier: 4.086A pdb=" N VAL F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.691A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.961A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 303 removed outlier: 6.712A pdb=" N LYS A 321 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 299 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 319 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS A 301 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL A 303 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER A 315 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AB2, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'A' and resid 387 through 388 removed outlier: 5.644A pdb=" N ARG B 295 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE B 315 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR B 297 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU B 313 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 299 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR B 311 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'B' and resid 35 through 39 removed outlier: 8.417A pdb=" N ILE B 35 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 52 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 37 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N SER B 52 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET B 71 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS B 67 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 39 removed outlier: 8.417A pdb=" N ILE B 35 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 52 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 37 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N ILE B 49 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N GLN B 108 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N VAL B 51 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 11.389A pdb=" N LEU B 106 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ALA B 53 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE B 104 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 57 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N HIS B 100 " --> pdb=" O TYR B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.516A pdb=" N SER B 114 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS B 132 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR B 116 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 130 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER B 118 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N CYS B 128 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 152 through 159 Processing sheet with id=AC1, first strand: chain 'B' and resid 241 through 242 removed outlier: 6.175A pdb=" N ILE B 261 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR B 169 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 259 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR B 171 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY B 257 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 184 through 186 removed outlier: 4.727A pdb=" N VAL B 191 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 219 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AC5, first strand: chain 'C' and resid 15 through 19 removed outlier: 5.644A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 35 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU C 45 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 47 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 140 through 147 removed outlier: 6.924A pdb=" N VAL C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 47 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU C 45 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 35 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AC8, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD1, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD2, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD3, first strand: chain 'C' and resid 296 through 303 removed outlier: 6.710A pdb=" N LYS C 321 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 299 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN C 319 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS C 301 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR C 317 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL C 303 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER C 315 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AD5, first strand: chain 'C' and resid 362 through 363 Processing sheet with id=AD6, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.534A pdb=" N THR D 279 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 387 through 388 removed outlier: 5.633A pdb=" N ARG D 295 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE D 315 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR D 297 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU D 313 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 299 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 311 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 6 through 7 removed outlier: 4.561A pdb=" N HIS D 260 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY D 257 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR D 171 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 259 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR D 169 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE D 261 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AE1, first strand: chain 'D' and resid 35 through 39 removed outlier: 8.429A pdb=" N ILE D 35 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER D 52 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N SER D 52 " --> pdb=" O MET D 71 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET D 71 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS D 67 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 35 through 39 removed outlier: 8.429A pdb=" N ILE D 35 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER D 52 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 11.458A pdb=" N ILE D 49 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N GLN D 108 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N VAL D 51 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N LEU D 106 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ALA D 53 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE D 104 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TYR D 57 " --> pdb=" O HIS D 100 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N HIS D 100 " --> pdb=" O TYR D 57 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 87 through 90 removed outlier: 5.405A pdb=" N LYS D 132 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR D 116 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL D 130 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER D 118 " --> pdb=" O CYS D 128 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS D 128 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 152 through 159 Processing sheet with id=AE5, first strand: chain 'D' and resid 184 through 186 removed outlier: 4.684A pdb=" N VAL D 191 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 219 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 210 through 215 Processing sheet with id=AE7, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AE8, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.647A pdb=" N ILE E 31 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 35 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AF1, first strand: chain 'E' and resid 42 through 48 removed outlier: 6.939A pdb=" N ALA E 121 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL E 47 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA E 119 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AF3, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AF4, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF5, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AF6, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'E' and resid 296 through 303 removed outlier: 6.694A pdb=" N LYS E 321 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL E 299 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN E 319 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS E 301 " --> pdb=" O THR E 317 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR E 317 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL E 303 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER E 315 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY E 350 " --> pdb=" O TYR E 320 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 330 through 332 Processing sheet with id=AF9, first strand: chain 'E' and resid 362 through 363 Processing sheet with id=AG1, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AG2, first strand: chain 'E' and resid 387 through 388 removed outlier: 5.611A pdb=" N ARG F 295 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE F 315 " --> pdb=" O ARG F 295 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR F 297 " --> pdb=" O GLU F 313 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU F 313 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU F 299 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR F 311 " --> pdb=" O LEU F 299 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 6 through 7 removed outlier: 4.570A pdb=" N HIS F 260 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY F 257 " --> pdb=" O THR F 171 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR F 171 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU F 259 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR F 169 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE F 261 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AG5, first strand: chain 'F' and resid 35 through 39 removed outlier: 8.469A pdb=" N ILE F 35 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER F 52 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN F 37 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N SER F 52 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET F 71 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LYS F 67 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 35 through 39 removed outlier: 8.469A pdb=" N ILE F 35 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER F 52 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN F 37 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 11.346A pdb=" N ILE F 49 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N GLN F 108 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N VAL F 51 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N LEU F 106 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N ALA F 53 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE F 104 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR F 57 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N HIS F 100 " --> pdb=" O TYR F 57 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.152A pdb=" N ASP F 113 " --> pdb=" O LYS F 132 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 152 through 159 Processing sheet with id=AG9, first strand: chain 'F' and resid 184 through 186 removed outlier: 4.723A pdb=" N VAL F 191 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR F 219 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 210 through 215 722 hydrogen bonds defined for protein. 1893 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: 3.50 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6368 1.34 - 1.46: 4859 1.46 - 1.59: 8885 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 20268 Sorted by residual: bond pdb=" C THR F 402 " pdb=" N PRO F 403 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.08e+00 bond pdb=" C THR D 402 " pdb=" N PRO D 403 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.08e+00 bond pdb=" C THR B 402 " pdb=" N PRO B 403 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.83e+00 bond pdb=" CA PRO C 382 " pdb=" C PRO C 382 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.62e+00 bond pdb=" CG1 ILE B 193 " pdb=" CD1 ILE B 193 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 ... (remaining 20263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 27346 2.45 - 4.90: 257 4.90 - 7.36: 14 7.36 - 9.81: 3 9.81 - 12.26: 1 Bond angle restraints: 27621 Sorted by residual: angle pdb=" C ASN B 243 " pdb=" N SER B 244 " pdb=" CA SER B 244 " ideal model delta sigma weight residual 121.27 133.53 -12.26 3.40e+00 8.65e-02 1.30e+01 angle pdb=" N ILE C 276 " pdb=" CA ILE C 276 " pdb=" C ILE C 276 " ideal model delta sigma weight residual 107.60 110.75 -3.15 1.07e+00 8.73e-01 8.69e+00 angle pdb=" N ILE E 276 " pdb=" CA ILE E 276 " pdb=" C ILE E 276 " ideal model delta sigma weight residual 107.60 110.47 -2.87 1.07e+00 8.73e-01 7.21e+00 angle pdb=" N ALA A 401 " pdb=" CA ALA A 401 " pdb=" C ALA A 401 " ideal model delta sigma weight residual 114.39 110.56 3.83 1.45e+00 4.76e-01 6.99e+00 angle pdb=" N ALA C 401 " pdb=" CA ALA C 401 " pdb=" C ALA C 401 " ideal model delta sigma weight residual 114.39 110.56 3.83 1.45e+00 4.76e-01 6.97e+00 ... (remaining 27616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11014 17.80 - 35.61: 841 35.61 - 53.41: 263 53.41 - 71.22: 46 71.22 - 89.02: 13 Dihedral angle restraints: 12177 sinusoidal: 4716 harmonic: 7461 Sorted by residual: dihedral pdb=" CB CYS B 156 " pdb=" SG CYS B 156 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual -86.00 -125.78 39.78 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS F 156 " pdb=" SG CYS F 156 " pdb=" SG CYS F 270 " pdb=" CB CYS F 270 " ideal model delta sinusoidal sigma weight residual -86.00 -125.03 39.03 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS D 156 " pdb=" SG CYS D 156 " pdb=" SG CYS D 270 " pdb=" CB CYS D 270 " ideal model delta sinusoidal sigma weight residual -86.00 -123.77 37.77 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 12174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1670 0.028 - 0.057: 894 0.057 - 0.085: 343 0.085 - 0.114: 149 0.114 - 0.142: 79 Chirality restraints: 3135 Sorted by residual: chirality pdb=" CA ILE E 55 " pdb=" N ILE E 55 " pdb=" C ILE E 55 " pdb=" CB ILE E 55 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE B 261 " pdb=" N ILE B 261 " pdb=" C ILE B 261 " pdb=" CB ILE B 261 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A 55 " pdb=" N ILE A 55 " pdb=" C ILE A 55 " pdb=" CB ILE A 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 3132 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 390 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 391 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 255 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 256 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 390 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 391 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " 0.020 5.00e-02 4.00e+02 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 132 2.63 - 3.20: 16148 3.20 - 3.76: 29434 3.76 - 4.33: 43049 4.33 - 4.90: 70198 Nonbonded interactions: 158961 Sorted by model distance: nonbonded pdb=" OE2 GLU B 131 " pdb=" NH1 ARG D 295 " model vdw 2.060 3.120 nonbonded pdb=" OE2 GLU D 131 " pdb=" NH1 ARG F 295 " model vdw 2.076 3.120 nonbonded pdb=" NH1 ARG B 295 " pdb=" OE2 GLU F 131 " model vdw 2.081 3.120 nonbonded pdb=" OG1 THR B 301 " pdb=" OG1 THR B 311 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR F 301 " pdb=" OG1 THR F 311 " model vdw 2.260 3.040 ... (remaining 158956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 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 : 0.003 0.046 20307 Z= 0.135 Angle : 0.600 12.261 27699 Z= 0.314 Chirality : 0.044 0.142 3135 Planarity : 0.006 0.046 3525 Dihedral : 14.327 89.019 7266 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.27 % Allowed : 10.71 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.16), residues: 2559 helix: -0.06 (0.30), residues: 273 sheet: -0.05 (0.17), residues: 858 loop : -1.08 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 141 TYR 0.023 0.002 TYR C 308 PHE 0.013 0.002 PHE E 189 TRP 0.016 0.002 TRP F 283 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00298 (20268) covalent geometry : angle 0.59845 (27621) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.09745 ( 78) hydrogen bonds : bond 0.19843 ( 654) hydrogen bonds : angle 7.77392 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 210 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 388 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8117 (pp) REVERT: B 338 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: C 220 ARG cc_start: 0.9170 (mmt90) cc_final: 0.8901 (mpt-90) REVERT: C 388 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8476 (tt) REVERT: D 24 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8374 (ptt180) REVERT: D 84 MET cc_start: 0.9457 (mmm) cc_final: 0.8996 (mmp) REVERT: D 120 THR cc_start: 0.9010 (m) cc_final: 0.8767 (p) REVERT: D 221 MET cc_start: 0.9089 (mmp) cc_final: 0.8841 (mmp) REVERT: D 355 TRP cc_start: 0.7825 (m100) cc_final: 0.7618 (m100) REVERT: D 369 VAL cc_start: 0.9295 (t) cc_final: 0.9080 (t) REVERT: E 220 ARG cc_start: 0.9198 (mmt90) cc_final: 0.8753 (mpt-90) REVERT: E 433 MET cc_start: 0.7240 (mmp) cc_final: 0.6831 (mmp) REVERT: F 84 MET cc_start: 0.9436 (mmm) cc_final: 0.8796 (mmm) REVERT: F 338 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8995 (mm-30) REVERT: F 373 ILE cc_start: 0.6873 (mt) cc_final: 0.6662 (mt) outliers start: 115 outliers final: 42 residues processed: 292 average time/residue: 0.5276 time to fit residues: 175.3586 Evaluate side-chains 226 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 1 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 382 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 93 GLN A 139 ASN A 270 ASN A 364 ASN A 386 HIS A 396 GLN A 408 ASN A 436 ASN B 77 HIS B 150 HIS B 250 HIS B 253 HIS B 260 HIS B 276 HIS B 336 ASN B 337 HIS B 345 GLN B 353 HIS C 59 GLN C 93 GLN C 139 ASN C 270 ASN C 386 HIS C 396 GLN C 408 ASN D 77 HIS D 108 GLN D 150 HIS D 250 HIS D 253 HIS D 260 HIS D 336 ASN D 337 HIS D 345 GLN D 353 HIS E 59 GLN E 93 GLN E 270 ASN E 364 ASN E 386 HIS E 396 GLN E 408 ASN E 436 ASN F 77 HIS F 108 GLN F 150 HIS F 250 HIS F 253 HIS F 260 HIS F 276 HIS F 336 ASN F 337 HIS F 345 GLN F 353 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.074102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.060125 restraints weight = 38840.542| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 1.48 r_work: 0.2574 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20307 Z= 0.109 Angle : 0.552 7.674 27699 Z= 0.288 Chirality : 0.043 0.144 3135 Planarity : 0.005 0.035 3525 Dihedral : 6.907 59.529 2847 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.57 % Allowed : 14.10 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2559 helix: 0.70 (0.31), residues: 270 sheet: 0.17 (0.18), residues: 840 loop : -0.87 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 289 TYR 0.020 0.001 TYR A 308 PHE 0.010 0.001 PHE E 356 TRP 0.013 0.001 TRP F 283 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00238 (20268) covalent geometry : angle 0.55103 (27621) SS BOND : bond 0.00242 ( 39) SS BOND : angle 0.92302 ( 78) hydrogen bonds : bond 0.04442 ( 654) hydrogen bonds : angle 5.56984 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: B 71 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8923 (tpt) REVERT: B 237 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: B 338 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: C 1 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7690 (p90) REVERT: C 254 THR cc_start: 0.9258 (m) cc_final: 0.8978 (p) REVERT: C 388 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8427 (tt) REVERT: D 24 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8346 (ptt180) REVERT: D 120 THR cc_start: 0.8976 (m) cc_final: 0.8601 (p) REVERT: D 220 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8909 (ttpm) REVERT: D 236 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: D 355 TRP cc_start: 0.8119 (m100) cc_final: 0.7917 (m100) REVERT: D 369 VAL cc_start: 0.9257 (t) cc_final: 0.9028 (t) REVERT: E 433 MET cc_start: 0.7487 (mmp) cc_final: 0.7222 (mmp) REVERT: F 59 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: F 84 MET cc_start: 0.9324 (mmm) cc_final: 0.8683 (mmm) REVERT: F 338 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8973 (mm-30) REVERT: F 373 ILE cc_start: 0.6885 (mt) cc_final: 0.6623 (mt) outliers start: 78 outliers final: 37 residues processed: 234 average time/residue: 0.5435 time to fit residues: 143.3471 Evaluate side-chains 217 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 1 PHE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 183 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 HIS F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.070512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.056305 restraints weight = 38869.614| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 1.42 r_work: 0.2466 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20307 Z= 0.215 Angle : 0.688 11.105 27699 Z= 0.358 Chirality : 0.048 0.174 3135 Planarity : 0.006 0.057 3525 Dihedral : 7.044 58.749 2820 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.90 % Allowed : 15.20 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2559 helix: 0.85 (0.30), residues: 294 sheet: -0.01 (0.17), residues: 828 loop : -0.95 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 141 TYR 0.028 0.002 TYR C 308 PHE 0.017 0.003 PHE E 189 TRP 0.018 0.002 TRP D 283 HIS 0.006 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00514 (20268) covalent geometry : angle 0.68668 (27621) SS BOND : bond 0.00529 ( 39) SS BOND : angle 1.11128 ( 78) hydrogen bonds : bond 0.04524 ( 654) hydrogen bonds : angle 5.39466 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 178 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 59 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: B 338 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: C 379 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: C 388 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8516 (tt) REVERT: D 73 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: D 220 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.8851 (ttpm) REVERT: D 355 TRP cc_start: 0.8407 (m100) cc_final: 0.8182 (m100) REVERT: E 29 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7961 (pt) REVERT: E 324 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.8045 (ptt-90) REVERT: E 339 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8818 (mp) REVERT: E 433 MET cc_start: 0.7547 (mmp) cc_final: 0.7325 (mmp) REVERT: F 59 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: F 84 MET cc_start: 0.9315 (mmm) cc_final: 0.8782 (mmm) REVERT: F 338 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: F 373 ILE cc_start: 0.7030 (mt) cc_final: 0.6709 (mt) outliers start: 107 outliers final: 57 residues processed: 244 average time/residue: 0.5962 time to fit residues: 164.2978 Evaluate side-chains 229 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 1 PHE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 200 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 245 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 0.0060 chunk 31 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 331 HIS B 108 GLN B 200 ASN E 396 GLN F 108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.071972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.057998 restraints weight = 38957.446| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 1.48 r_work: 0.2511 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20307 Z= 0.125 Angle : 0.576 11.586 27699 Z= 0.296 Chirality : 0.044 0.157 3135 Planarity : 0.005 0.041 3525 Dihedral : 6.419 59.744 2811 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.26 % Allowed : 16.71 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2559 helix: 1.10 (0.30), residues: 294 sheet: 0.04 (0.18), residues: 831 loop : -0.82 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 398 TYR 0.021 0.001 TYR C 308 PHE 0.011 0.001 PHE E 189 TRP 0.011 0.001 TRP D 283 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00290 (20268) covalent geometry : angle 0.57524 (27621) SS BOND : bond 0.00303 ( 39) SS BOND : angle 0.80660 ( 78) hydrogen bonds : bond 0.03719 ( 654) hydrogen bonds : angle 5.05637 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 170 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 434 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6607 (pp) REVERT: B 59 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: B 338 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: D 73 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: D 220 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.8926 (ttpm) REVERT: D 238 THR cc_start: 0.8247 (p) cc_final: 0.7940 (p) REVERT: D 355 TRP cc_start: 0.8324 (m100) cc_final: 0.8119 (m100) REVERT: E 324 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.8018 (ptt-90) REVERT: E 434 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6727 (pp) REVERT: F 59 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: F 84 MET cc_start: 0.9276 (mmm) cc_final: 0.8733 (mmm) REVERT: F 238 THR cc_start: 0.7916 (p) cc_final: 0.7706 (p) REVERT: F 338 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: F 373 ILE cc_start: 0.6918 (mt) cc_final: 0.6666 (mt) outliers start: 93 outliers final: 53 residues processed: 234 average time/residue: 0.5923 time to fit residues: 156.5950 Evaluate side-chains 220 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 136 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 396 GLN D 200 ASN F 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.071373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.057589 restraints weight = 39083.894| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 1.51 r_work: 0.2474 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20307 Z= 0.250 Angle : 0.727 13.640 27699 Z= 0.376 Chirality : 0.050 0.219 3135 Planarity : 0.007 0.068 3525 Dihedral : 6.851 58.863 2806 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 16.30 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2559 helix: 0.98 (0.30), residues: 294 sheet: -0.05 (0.17), residues: 831 loop : -0.94 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 289 TYR 0.029 0.002 TYR C 308 PHE 0.019 0.003 PHE E 189 TRP 0.018 0.003 TRP F 39 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00611 (20268) covalent geometry : angle 0.72512 (27621) SS BOND : bond 0.00631 ( 39) SS BOND : angle 1.15611 ( 78) hydrogen bonds : bond 0.04383 ( 654) hydrogen bonds : angle 5.28830 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 159 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 293 SER cc_start: 0.8951 (t) cc_final: 0.8709 (p) REVERT: B 59 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: B 338 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: C 324 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7728 (ptt180) REVERT: D 24 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8447 (ptt180) REVERT: D 59 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8827 (tm-30) REVERT: D 73 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: D 220 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.8953 (ttpm) REVERT: D 355 TRP cc_start: 0.8361 (m100) cc_final: 0.8153 (m100) REVERT: E 29 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8051 (pt) REVERT: E 293 SER cc_start: 0.8838 (t) cc_final: 0.8510 (p) REVERT: E 324 ARG cc_start: 0.8170 (ptt-90) cc_final: 0.7965 (ptt-90) REVERT: F 59 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: F 84 MET cc_start: 0.9306 (mmm) cc_final: 0.8717 (mmm) REVERT: F 108 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8851 (tp40) REVERT: F 338 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: F 373 ILE cc_start: 0.7068 (mt) cc_final: 0.6743 (mt) outliers start: 119 outliers final: 84 residues processed: 242 average time/residue: 0.5709 time to fit residues: 157.9184 Evaluate side-chains 250 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 156 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 324 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain E residue 433 MET Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 250 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN C 396 GLN D 357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.073116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.059377 restraints weight = 38973.310| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 1.49 r_work: 0.2516 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20307 Z= 0.138 Angle : 0.601 13.087 27699 Z= 0.306 Chirality : 0.045 0.184 3135 Planarity : 0.005 0.045 3525 Dihedral : 6.437 59.788 2805 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.67 % Allowed : 17.67 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2559 helix: 1.20 (0.30), residues: 294 sheet: -0.02 (0.18), residues: 828 loop : -0.83 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 398 TYR 0.022 0.002 TYR C 308 PHE 0.012 0.002 PHE E 189 TRP 0.011 0.002 TRP B 283 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00324 (20268) covalent geometry : angle 0.60039 (27621) SS BOND : bond 0.00311 ( 39) SS BOND : angle 0.75727 ( 78) hydrogen bonds : bond 0.03737 ( 654) hydrogen bonds : angle 5.03002 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 162 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 139 ASN cc_start: 0.7544 (t0) cc_final: 0.7336 (t0) REVERT: A 293 SER cc_start: 0.8926 (t) cc_final: 0.8680 (p) REVERT: A 434 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6522 (pp) REVERT: B 59 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: B 338 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: C 396 GLN cc_start: 0.9057 (tt0) cc_final: 0.8855 (mt0) REVERT: D 24 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8428 (ptt180) REVERT: D 73 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8826 (m-80) REVERT: D 220 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.8906 (ttpm) REVERT: D 355 TRP cc_start: 0.8307 (m100) cc_final: 0.8103 (m100) REVERT: D 398 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.8012 (ttp80) REVERT: E 29 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7963 (pt) REVERT: E 293 SER cc_start: 0.8824 (t) cc_final: 0.8480 (p) REVERT: F 59 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: F 338 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8337 (mp0) outliers start: 102 outliers final: 72 residues processed: 234 average time/residue: 0.5630 time to fit residues: 150.4024 Evaluate side-chains 239 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain E residue 433 MET Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 169 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 238 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.074609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.061007 restraints weight = 39269.805| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 1.47 r_work: 0.2566 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20307 Z= 0.095 Angle : 0.547 11.669 27699 Z= 0.276 Chirality : 0.043 0.203 3135 Planarity : 0.005 0.046 3525 Dihedral : 5.979 59.866 2805 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.43 % Allowed : 18.91 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2559 helix: 1.42 (0.30), residues: 294 sheet: 0.16 (0.18), residues: 828 loop : -0.68 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 289 TYR 0.018 0.001 TYR C 308 PHE 0.010 0.001 PHE A 95 TRP 0.009 0.001 TRP B 283 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00212 (20268) covalent geometry : angle 0.54379 (27621) SS BOND : bond 0.00243 ( 39) SS BOND : angle 1.24421 ( 78) hydrogen bonds : bond 0.03262 ( 654) hydrogen bonds : angle 4.78343 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 139 ASN cc_start: 0.7521 (t0) cc_final: 0.7300 (t0) REVERT: A 195 MET cc_start: 0.8621 (mtm) cc_final: 0.8121 (mtm) REVERT: A 434 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6524 (pp) REVERT: B 59 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: B 338 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: D 24 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8407 (ptt180) REVERT: D 73 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8784 (m-80) REVERT: D 220 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8865 (ttpm) REVERT: D 395 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8663 (ttpp) REVERT: D 398 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7758 (ttp80) REVERT: E 293 SER cc_start: 0.8788 (t) cc_final: 0.8587 (p) REVERT: E 339 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8657 (mt) REVERT: F 59 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: F 84 MET cc_start: 0.9234 (mmm) cc_final: 0.8651 (mmm) REVERT: F 338 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8249 (mp0) outliers start: 75 outliers final: 49 residues processed: 217 average time/residue: 0.5649 time to fit residues: 139.2528 Evaluate side-chains 221 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 192 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 160 optimal weight: 0.1980 chunk 9 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.073493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.059807 restraints weight = 39020.360| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 1.47 r_work: 0.2533 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20307 Z= 0.130 Angle : 0.587 11.571 27699 Z= 0.297 Chirality : 0.044 0.175 3135 Planarity : 0.005 0.044 3525 Dihedral : 6.101 59.791 2802 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.03 % Allowed : 18.45 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2559 helix: 1.45 (0.30), residues: 294 sheet: 0.13 (0.18), residues: 828 loop : -0.67 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 398 TYR 0.021 0.002 TYR C 308 PHE 0.012 0.002 PHE E 189 TRP 0.011 0.001 TRP D 283 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00308 (20268) covalent geometry : angle 0.58495 (27621) SS BOND : bond 0.00357 ( 39) SS BOND : angle 1.07347 ( 78) hydrogen bonds : bond 0.03518 ( 654) hydrogen bonds : angle 4.82647 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 165 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 139 ASN cc_start: 0.7569 (t0) cc_final: 0.7329 (t0) REVERT: A 293 SER cc_start: 0.8921 (t) cc_final: 0.8663 (p) REVERT: A 434 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6554 (pp) REVERT: B 59 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: B 338 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: D 24 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8461 (ptt180) REVERT: D 73 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: D 220 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8930 (ttpm) REVERT: E 293 SER cc_start: 0.8891 (t) cc_final: 0.8651 (p) REVERT: F 59 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: F 338 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: F 395 LYS cc_start: 0.9095 (tppp) cc_final: 0.8736 (tppp) outliers start: 88 outliers final: 66 residues processed: 227 average time/residue: 0.5761 time to fit residues: 149.0815 Evaluate side-chains 236 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 195 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN F 108 GLN F 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.073783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.060143 restraints weight = 39008.685| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 1.48 r_work: 0.2544 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20307 Z= 0.118 Angle : 0.572 11.765 27699 Z= 0.288 Chirality : 0.044 0.164 3135 Planarity : 0.005 0.049 3525 Dihedral : 6.013 59.581 2802 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.71 % Allowed : 18.86 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2559 helix: 1.46 (0.30), residues: 294 sheet: 0.12 (0.18), residues: 834 loop : -0.61 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 398 TYR 0.020 0.001 TYR A 308 PHE 0.011 0.001 PHE E 189 TRP 0.009 0.001 TRP B 283 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00277 (20268) covalent geometry : angle 0.57071 (27621) SS BOND : bond 0.00305 ( 39) SS BOND : angle 0.92015 ( 78) hydrogen bonds : bond 0.03437 ( 654) hydrogen bonds : angle 4.78403 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 161 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 195 MET cc_start: 0.8648 (mtm) cc_final: 0.8184 (mtm) REVERT: A 293 SER cc_start: 0.8930 (t) cc_final: 0.8666 (p) REVERT: A 434 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6512 (pp) REVERT: B 59 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: B 338 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: D 24 ARG cc_start: 0.8752 (ptt180) cc_final: 0.8461 (ptt180) REVERT: D 73 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: D 220 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.8938 (ttpm) REVERT: D 236 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: E 293 SER cc_start: 0.8904 (t) cc_final: 0.8656 (p) REVERT: F 59 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: F 338 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8284 (mp0) outliers start: 81 outliers final: 69 residues processed: 223 average time/residue: 0.5283 time to fit residues: 135.0080 Evaluate side-chains 235 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 433 MET Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 183 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 206 optimal weight: 0.0370 chunk 127 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 108 GLN F 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.071805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.058059 restraints weight = 39250.587| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 1.48 r_work: 0.2477 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20307 Z= 0.215 Angle : 0.699 13.952 27699 Z= 0.358 Chirality : 0.048 0.207 3135 Planarity : 0.006 0.061 3525 Dihedral : 6.495 59.445 2798 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.89 % Allowed : 18.82 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2559 helix: 1.24 (0.30), residues: 294 sheet: -0.01 (0.18), residues: 828 loop : -0.81 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 398 TYR 0.028 0.002 TYR C 308 PHE 0.018 0.003 PHE E 189 TRP 0.015 0.002 TRP F 39 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00523 (20268) covalent geometry : angle 0.69711 (27621) SS BOND : bond 0.00585 ( 39) SS BOND : angle 1.22695 ( 78) hydrogen bonds : bond 0.04132 ( 654) hydrogen bonds : angle 5.09285 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 164 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 293 SER cc_start: 0.9008 (t) cc_final: 0.8803 (p) REVERT: A 434 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6528 (pp) REVERT: B 59 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: B 338 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: D 24 ARG cc_start: 0.8793 (ptt180) cc_final: 0.8511 (ptt180) REVERT: D 220 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.8996 (ttpm) REVERT: D 398 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7673 (ttp-110) REVERT: F 59 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: F 338 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8348 (mp0) outliers start: 85 outliers final: 73 residues processed: 228 average time/residue: 0.5537 time to fit residues: 143.1812 Evaluate side-chains 237 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 158 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 433 MET Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.058398 restraints weight = 39219.517| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 1.50 r_work: 0.2491 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20307 Z= 0.178 Angle : 0.661 13.950 27699 Z= 0.337 Chirality : 0.047 0.195 3135 Planarity : 0.006 0.049 3525 Dihedral : 6.420 59.381 2798 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.85 % Allowed : 19.18 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2559 helix: 1.26 (0.30), residues: 294 sheet: -0.03 (0.18), residues: 828 loop : -0.83 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 289 TYR 0.024 0.002 TYR C 308 PHE 0.016 0.002 PHE E 189 TRP 0.013 0.002 TRP F 39 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00427 (20268) covalent geometry : angle 0.65949 (27621) SS BOND : bond 0.00475 ( 39) SS BOND : angle 1.06361 ( 78) hydrogen bonds : bond 0.03936 ( 654) hydrogen bonds : angle 5.05292 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8031.32 seconds wall clock time: 137 minutes 13.19 seconds (8233.19 seconds total)