Starting phenix.real_space_refine on Sat Feb 7 23:22:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uga_64134/02_2026/9uga_64134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uga_64134/02_2026/9uga_64134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uga_64134/02_2026/9uga_64134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uga_64134/02_2026/9uga_64134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uga_64134/02_2026/9uga_64134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uga_64134/02_2026/9uga_64134.map" } resolution = 3.06 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= -0.000 sd= 0.017 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 152 5.16 5 C 23416 2.51 5 N 6664 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.04s 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: 36976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "D" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "E" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "F" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "G" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "H" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Time building chain proxies: 8.50, per 1000 atoms: 0.23 Number of scatterers: 36976 At special positions: 0 Unit cell: (209.526, 209.526, 84.702, 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 152 16.00 O 6744 8.00 N 6664 7.00 C 23416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 343 helices and 8 sheets defined 74.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.511A pdb=" N ALA A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.725A pdb=" N ALA A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.771A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.384A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.824A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.556A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.282A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.520A pdb=" N TRP A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.550A pdb=" N TRP A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 290 through 294 removed outlier: 6.136A pdb=" N LEU A 293 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.574A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.819A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.635A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 424 through 425 No H-bonds generated for 'chain 'A' and resid 424 through 425' Processing helix chain 'A' and resid 426 through 429 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.723A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.889A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.679A pdb=" N LEU A 515 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N HIS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.509A pdb=" N LEU A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 573 through 587 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.615A pdb=" N CYS A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'B' and resid 62 through 68 removed outlier: 4.323A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.635A pdb=" N ALA B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 104 removed outlier: 3.782A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.852A pdb=" N GLN B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 141 through 151 removed outlier: 3.808A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.544A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 3.764A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.658A pdb=" N TRP B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 290 through 294 removed outlier: 6.072A pdb=" N LEU B 293 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.622A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.679A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 326 through 329 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.593A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.989A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 381 removed outlier: 3.638A pdb=" N TYR B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 424 through 425 No H-bonds generated for 'chain 'B' and resid 424 through 425' Processing helix chain 'B' and resid 426 through 429 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.582A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.833A pdb=" N ARG B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.873A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.587A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 543 Processing helix chain 'B' and resid 573 through 587 Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.895A pdb=" N CYS B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.528A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 4.228A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.663A pdb=" N ALA C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 104 removed outlier: 3.607A pdb=" N ALA C 93 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.818A pdb=" N GLN C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.955A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.590A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 177 through 193 removed outlier: 3.669A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.636A pdb=" N TRP C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 238 through 248 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 290 through 294 removed outlier: 6.157A pdb=" N LEU C 293 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.562A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.530A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 309' Processing helix chain 'C' and resid 323 through 328 removed outlier: 3.559A pdb=" N GLN C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.596A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 359 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.761A pdb=" N ASP C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.648A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 425 through 429 removed outlier: 5.427A pdb=" N LYS C 428 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 437 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.501A pdb=" N ARG C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 461 through 477 Processing helix chain 'C' and resid 486 through 495 Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 511 through 518 removed outlier: 3.525A pdb=" N LEU C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 543 Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 573 through 587 Processing helix chain 'C' and resid 606 through 614 Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.804A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 699 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.681A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 104 removed outlier: 3.807A pdb=" N ALA D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.930A pdb=" N GLN D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.584A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 4.243A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 206 through 214 Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.507A pdb=" N TRP D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 283 through 289 Processing helix chain 'D' and resid 290 through 294 removed outlier: 6.118A pdb=" N LEU D 293 " --> pdb=" O SER D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.705A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.605A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.747A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 425 through 429 removed outlier: 5.057A pdb=" N LYS D 428 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 461 through 477 Processing helix chain 'D' and resid 486 through 495 Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.657A pdb=" N ARG D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.895A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 543 Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 573 through 587 Processing helix chain 'D' and resid 606 through 614 removed outlier: 3.662A pdb=" N MET D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.538A pdb=" N CYS D 649 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 699 Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'E' and resid 71 through 79 Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.768A pdb=" N ALA E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.715A pdb=" N GLN E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 141 through 151 removed outlier: 3.621A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.562A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 177 through 193 removed outlier: 4.025A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.637A pdb=" N TRP E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 238 through 248 Processing helix chain 'E' and resid 250 through 253 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 289 Processing helix chain 'E' and resid 290 through 294 removed outlier: 6.164A pdb=" N LEU E 293 " --> pdb=" O SER E 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 294 " --> pdb=" O GLY E 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 290 through 294' Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.559A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.571A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 309' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.545A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 359 Processing helix chain 'E' and resid 363 through 369 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.651A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 425 through 429 removed outlier: 5.337A pdb=" N LYS E 428 " --> pdb=" O GLY E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 437 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.534A pdb=" N ARG E 445 " --> pdb=" O ASP E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 461 through 477 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.773A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.581A pdb=" N ARG E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 500' Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 514 through 518 Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 543 Processing helix chain 'E' and resid 544 through 546 No H-bonds generated for 'chain 'E' and resid 544 through 546' Processing helix chain 'E' and resid 573 through 587 Processing helix chain 'E' and resid 606 through 614 removed outlier: 3.836A pdb=" N MET E 612 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.633A pdb=" N CYS E 649 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 699 Processing helix chain 'F' and resid 62 through 68 removed outlier: 4.213A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.763A pdb=" N ALA F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 104 removed outlier: 3.624A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.809A pdb=" N GLN F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 141 through 151 removed outlier: 3.821A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.609A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 177 through 193 removed outlier: 3.674A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 Processing helix chain 'F' and resid 206 through 214 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 249 through 254 removed outlier: 3.518A pdb=" N TRP F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 283 through 291 removed outlier: 3.710A pdb=" N SER F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY F 291 " --> pdb=" O VAL F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.533A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 359 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.590A pdb=" N ASP F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 381 removed outlier: 3.625A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 398 Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 424 through 425 No H-bonds generated for 'chain 'F' and resid 424 through 425' Processing helix chain 'F' and resid 426 through 429 Processing helix chain 'F' and resid 430 through 437 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 461 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.697A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.770A pdb=" N ARG F 499 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.827A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.556A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 526 Processing helix chain 'F' and resid 531 through 543 Processing helix chain 'F' and resid 573 through 587 Processing helix chain 'F' and resid 606 through 614 Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.530A pdb=" N CYS F 649 " --> pdb=" O THR F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 690 through 699 Processing helix chain 'G' and resid 62 through 68 removed outlier: 4.353A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 3.507A pdb=" N ALA G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.611A pdb=" N ALA G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.669A pdb=" N GLN G 114 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 141 through 151 removed outlier: 3.822A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 removed outlier: 3.524A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 172 removed outlier: 4.016A pdb=" N LEU G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 193 removed outlier: 3.737A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 206 through 214 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 238 through 248 Processing helix chain 'G' and resid 250 through 253 Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 289 Processing helix chain 'G' and resid 290 through 295 removed outlier: 6.158A pdb=" N LEU G 293 " --> pdb=" O SER G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 303 Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.515A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA G 309 " --> pdb=" O PRO G 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 309' Processing helix chain 'G' and resid 323 through 328 removed outlier: 3.784A pdb=" N GLN G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.508A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 359 Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.614A pdb=" N ASP G 367 " --> pdb=" O LYS G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.568A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR G 380 " --> pdb=" O ARG G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 398 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 425 through 429 removed outlier: 5.126A pdb=" N LYS G 428 " --> pdb=" O GLY G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 437 Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 461 through 477 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.613A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.832A pdb=" N ARG G 499 " --> pdb=" O PRO G 496 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 496 through 500' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 511 through 518 removed outlier: 3.697A pdb=" N LEU G 515 " --> pdb=" O ARG G 512 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS G 516 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 543 Processing helix chain 'G' and resid 573 through 587 Processing helix chain 'G' and resid 606 through 614 Processing helix chain 'G' and resid 638 through 650 removed outlier: 3.964A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 699 Processing helix chain 'H' and resid 62 through 68 removed outlier: 4.226A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 Processing helix chain 'H' and resid 84 through 104 removed outlier: 3.583A pdb=" N GLU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.787A pdb=" N GLN H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 141 through 151 removed outlier: 3.823A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 removed outlier: 4.063A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 Processing helix chain 'H' and resid 177 through 193 removed outlier: 3.752A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 206 through 214 removed outlier: 3.574A pdb=" N TRP H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 238 through 248 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 264 through 278 Processing helix chain 'H' and resid 283 through 289 Processing helix chain 'H' and resid 290 through 294 removed outlier: 6.136A pdb=" N LEU H 293 " --> pdb=" O SER H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.928A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 328 removed outlier: 3.504A pdb=" N GLN H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.532A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 359 Processing helix chain 'H' and resid 363 through 369 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.752A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR H 380 " --> pdb=" O ARG H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 425 through 429 removed outlier: 5.357A pdb=" N LYS H 428 " --> pdb=" O GLY H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 437 Processing helix chain 'H' and resid 439 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 461 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.663A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.892A pdb=" N ARG H 499 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 496 through 500' Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 514 through 518 Processing helix chain 'H' and resid 519 through 526 removed outlier: 3.506A pdb=" N LEU H 524 " --> pdb=" O GLU H 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 544 removed outlier: 3.695A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 587 Processing helix chain 'H' and resid 606 through 614 Processing helix chain 'H' and resid 638 through 650 removed outlier: 3.750A pdb=" N CYS H 649 " --> pdb=" O THR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 699 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.118A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 681 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 592 through 593 removed outlier: 6.829A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 593 removed outlier: 3.683A pdb=" N PHE C 592 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 566 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 619 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 681 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.773A pdb=" N ILE D 681 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.834A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE E 617 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE E 656 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU E 619 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 564 through 567 removed outlier: 6.138A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU F 619 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE F 681 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 7.034A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU G 619 " --> pdb=" O VAL G 654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.898A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL H 654 " --> pdb=" O PHE H 617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE H 681 " --> pdb=" O PRO H 655 " (cutoff:3.500A) 2006 hydrogen bonds defined for protein. 5913 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: 8.38 Time building geometry restraints manager: 3.96 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: 12577 1.34 - 1.46: 7384 1.46 - 1.58: 17399 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 37552 Sorted by residual: bond pdb=" CG GLU H 100 " pdb=" CD GLU H 100 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.44e+00 bond pdb=" CB PRO G 177 " pdb=" CG PRO G 177 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 bond pdb=" CA PHE H 592 " pdb=" CB PHE H 592 " ideal model delta sigma weight residual 1.530 1.552 -0.023 1.57e-02 4.06e+03 2.12e+00 bond pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.09e+00 bond pdb=" N GLU H 100 " pdb=" CA GLU H 100 " ideal model delta sigma weight residual 1.459 1.476 -0.017 1.19e-02 7.06e+03 2.06e+00 ... (remaining 37547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 50104 2.45 - 4.91: 565 4.91 - 7.36: 55 7.36 - 9.81: 3 9.81 - 12.27: 1 Bond angle restraints: 50728 Sorted by residual: angle pdb=" N THR F 382 " pdb=" CA THR F 382 " pdb=" C THR F 382 " ideal model delta sigma weight residual 114.04 107.90 6.14 1.24e+00 6.50e-01 2.45e+01 angle pdb=" CA PRO G 177 " pdb=" N PRO G 177 " pdb=" CD PRO G 177 " ideal model delta sigma weight residual 112.00 105.34 6.66 1.40e+00 5.10e-01 2.27e+01 angle pdb=" N GLU H 100 " pdb=" CA GLU H 100 " pdb=" CB GLU H 100 " ideal model delta sigma weight residual 110.01 116.10 -6.09 1.45e+00 4.76e-01 1.77e+01 angle pdb=" N THR D 382 " pdb=" CA THR D 382 " pdb=" C THR D 382 " ideal model delta sigma weight residual 113.02 107.37 5.65 1.49e+00 4.50e-01 1.44e+01 angle pdb=" N VAL H 108 " pdb=" CA VAL H 108 " pdb=" C VAL H 108 " ideal model delta sigma weight residual 113.20 109.69 3.51 9.60e-01 1.09e+00 1.34e+01 ... (remaining 50723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 20316 17.97 - 35.94: 2090 35.94 - 53.91: 332 53.91 - 71.89: 71 71.89 - 89.86: 31 Dihedral angle restraints: 22840 sinusoidal: 9296 harmonic: 13544 Sorted by residual: dihedral pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" N ALA B 107 " pdb=" CA ALA B 107 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA PRO C 106 " pdb=" C PRO C 106 " pdb=" N ALA C 107 " pdb=" CA ALA C 107 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PRO G 106 " pdb=" C PRO G 106 " pdb=" N ALA G 107 " pdb=" CA ALA G 107 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 22837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4983 0.056 - 0.111: 783 0.111 - 0.167: 75 0.167 - 0.222: 3 0.222 - 0.278: 4 Chirality restraints: 5848 Sorted by residual: chirality pdb=" CA GLU A 100 " pdb=" N GLU A 100 " pdb=" C GLU A 100 " pdb=" CB GLU A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA GLU H 100 " pdb=" N GLU H 100 " pdb=" C GLU H 100 " pdb=" CB GLU H 100 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL H 99 " pdb=" CA VAL H 99 " pdb=" CG1 VAL H 99 " pdb=" CG2 VAL H 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5845 not shown) Planarity restraints: 6536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 176 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO G 177 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 654 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO G 655 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 655 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 655 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 97 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C GLN A 97 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN A 97 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 98 " 0.014 2.00e-02 2.50e+03 ... (remaining 6533 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2940 2.74 - 3.28: 37822 3.28 - 3.82: 58815 3.82 - 4.36: 68719 4.36 - 4.90: 119496 Nonbonded interactions: 287792 Sorted by model distance: nonbonded pdb=" OG SER G 572 " pdb=" OG SER G 622 " model vdw 2.197 3.040 nonbonded pdb=" NE2 GLN G 74 " pdb=" OE2 GLU G 94 " model vdw 2.219 3.120 nonbonded pdb=" OG SER F 572 " pdb=" OG SER F 622 " model vdw 2.225 3.040 nonbonded pdb=" OG SER C 572 " pdb=" OG SER C 622 " model vdw 2.229 3.040 nonbonded pdb=" O THR E 481 " pdb=" NZ LYS F 281 " model vdw 2.231 3.120 ... (remaining 287787 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 13.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.930 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.076 37552 Z= 0.163 Angle : 0.664 12.268 50728 Z= 0.380 Chirality : 0.040 0.278 5848 Planarity : 0.005 0.113 6536 Dihedral : 14.704 89.857 14040 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.31 (0.13), residues: 4624 helix: 0.41 (0.10), residues: 3224 sheet: -2.05 (0.38), residues: 160 loop : -1.35 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 249 TYR 0.013 0.001 TYR E 213 PHE 0.018 0.001 PHE B 347 TRP 0.015 0.001 TRP A 103 HIS 0.010 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00343 (37552) covalent geometry : angle 0.66384 (50728) hydrogen bonds : bond 0.12906 ( 2006) hydrogen bonds : angle 4.77671 ( 5913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7441 (tp30) REVERT: C 592 PHE cc_start: 0.6378 (t80) cc_final: 0.6152 (t80) REVERT: C 685 HIS cc_start: 0.6698 (m90) cc_final: 0.6380 (m-70) REVERT: D 261 LYS cc_start: 0.6708 (tptt) cc_final: 0.6396 (mmtm) REVERT: E 696 ILE cc_start: 0.7980 (mt) cc_final: 0.7771 (tt) REVERT: G 155 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7324 (pt0) REVERT: G 249 ARG cc_start: 0.6990 (mmm160) cc_final: 0.6731 (mmm-85) REVERT: H 156 ASN cc_start: 0.8210 (m-40) cc_final: 0.7941 (m110) REVERT: H 170 ASN cc_start: 0.7532 (m-40) cc_final: 0.6357 (p0) REVERT: H 565 PHE cc_start: 0.7155 (t80) cc_final: 0.6841 (t80) REVERT: H 592 PHE cc_start: 0.7895 (t80) cc_final: 0.7686 (t80) REVERT: H 652 ASN cc_start: 0.6078 (m110) cc_final: 0.5498 (m-40) REVERT: H 685 HIS cc_start: 0.6905 (t-90) cc_final: 0.6274 (t-90) outliers start: 2 outliers final: 0 residues processed: 396 average time/residue: 0.2217 time to fit residues: 141.8720 Evaluate side-chains 299 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 383 ASN B 685 HIS C 280 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN H 74 GLN H 383 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.175359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115853 restraints weight = 56068.310| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.92 r_work: 0.3294 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37552 Z= 0.151 Angle : 0.572 12.605 50728 Z= 0.289 Chirality : 0.039 0.165 5848 Planarity : 0.004 0.066 6536 Dihedral : 4.291 22.512 5128 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.05 % Allowed : 7.04 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.13), residues: 4624 helix: 0.61 (0.10), residues: 3200 sheet: -1.88 (0.39), residues: 160 loop : -1.17 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 249 TYR 0.013 0.001 TYR E 213 PHE 0.018 0.001 PHE G 565 TRP 0.010 0.001 TRP A 103 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00366 (37552) covalent geometry : angle 0.57201 (50728) hydrogen bonds : bond 0.04089 ( 2006) hydrogen bonds : angle 4.12941 ( 5913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 353 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7594 (tmm-80) REVERT: A 179 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7414 (tp30) REVERT: A 698 PHE cc_start: 0.4509 (OUTLIER) cc_final: 0.4120 (m-80) REVERT: B 96 PHE cc_start: 0.7303 (t80) cc_final: 0.6957 (t80) REVERT: C 592 PHE cc_start: 0.6116 (t80) cc_final: 0.5770 (t80) REVERT: D 261 LYS cc_start: 0.6600 (tptt) cc_final: 0.6238 (mmtm) REVERT: E 94 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: F 520 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8623 (tp30) REVERT: G 94 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.5022 (mm-30) REVERT: G 155 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7152 (pt0) REVERT: G 183 SER cc_start: 0.6441 (m) cc_final: 0.6099 (t) REVERT: G 394 LEU cc_start: 0.8836 (mt) cc_final: 0.8575 (mp) REVERT: H 97 GLN cc_start: 0.6927 (tp40) cc_final: 0.6672 (mm110) REVERT: H 565 PHE cc_start: 0.7339 (t80) cc_final: 0.7007 (t80) REVERT: H 592 PHE cc_start: 0.7406 (t80) cc_final: 0.7166 (t80) REVERT: H 685 HIS cc_start: 0.6778 (t-90) cc_final: 0.6092 (t-90) outliers start: 41 outliers final: 23 residues processed: 374 average time/residue: 0.2268 time to fit residues: 137.6540 Evaluate side-chains 336 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 307 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 403 optimal weight: 0.9990 chunk 423 optimal weight: 9.9990 chunk 395 optimal weight: 4.9990 chunk 461 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 HIS ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.168739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109441 restraints weight = 56968.947| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.81 r_work: 0.3226 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 37552 Z= 0.271 Angle : 0.654 13.501 50728 Z= 0.330 Chirality : 0.043 0.161 5848 Planarity : 0.005 0.057 6536 Dihedral : 4.567 22.077 5128 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.07 % Allowed : 11.07 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.13), residues: 4624 helix: 0.36 (0.09), residues: 3216 sheet: -1.84 (0.39), residues: 160 loop : -1.38 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 249 TYR 0.017 0.002 TYR C 380 PHE 0.026 0.002 PHE F 308 TRP 0.011 0.001 TRP C 683 HIS 0.005 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00662 (37552) covalent geometry : angle 0.65374 (50728) hydrogen bonds : bond 0.05076 ( 2006) hydrogen bonds : angle 4.37912 ( 5913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 339 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: A 146 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7372 (tmt170) REVERT: B 280 ASN cc_start: 0.8424 (t0) cc_final: 0.8207 (t0) REVERT: B 376 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7961 (ttm-80) REVERT: C 592 PHE cc_start: 0.6073 (t80) cc_final: 0.5821 (t80) REVERT: C 685 HIS cc_start: 0.6856 (m-70) cc_final: 0.6592 (m-70) REVERT: D 101 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: D 235 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7652 (mp) REVERT: E 86 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.7322 (ttm-80) REVERT: E 325 ASP cc_start: 0.7401 (t0) cc_final: 0.7157 (p0) REVERT: E 363 LYS cc_start: 0.7139 (mptt) cc_final: 0.6896 (pttm) REVERT: G 94 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5078 (mm-30) REVERT: G 155 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7306 (pt0) REVERT: G 259 PHE cc_start: 0.7983 (t80) cc_final: 0.7590 (t80) REVERT: G 308 PHE cc_start: 0.7752 (t80) cc_final: 0.7169 (t80) REVERT: G 399 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6945 (pm20) REVERT: H 97 GLN cc_start: 0.6864 (tp40) cc_final: 0.6504 (mm-40) REVERT: H 100 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: H 252 GLU cc_start: 0.8368 (tp30) cc_final: 0.8043 (tp30) REVERT: H 372 GLN cc_start: 0.7598 (mm-40) cc_final: 0.6606 (tp40) REVERT: H 565 PHE cc_start: 0.7307 (t80) cc_final: 0.6833 (t80) REVERT: H 579 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7700 (mm) REVERT: H 592 PHE cc_start: 0.7352 (t80) cc_final: 0.7126 (t80) REVERT: H 685 HIS cc_start: 0.6400 (t-90) cc_final: 0.5555 (t-90) outliers start: 81 outliers final: 36 residues processed: 395 average time/residue: 0.2313 time to fit residues: 147.7939 Evaluate side-chains 349 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 ASN Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 300 optimal weight: 20.0000 chunk 394 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 214 optimal weight: 0.6980 chunk 379 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 466 optimal weight: 7.9990 chunk 383 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN B 200 GLN B 571 ASN B 685 HIS C 616 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.172666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115024 restraints weight = 56818.213| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.20 r_work: 0.3334 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37552 Z= 0.128 Angle : 0.543 14.008 50728 Z= 0.272 Chirality : 0.038 0.177 5848 Planarity : 0.004 0.053 6536 Dihedral : 4.204 22.364 5128 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.94 % Allowed : 12.86 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.13), residues: 4624 helix: 0.66 (0.10), residues: 3216 sheet: -1.72 (0.39), residues: 160 loop : -1.20 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 249 TYR 0.010 0.001 TYR E 213 PHE 0.017 0.001 PHE A 565 TRP 0.009 0.001 TRP C 683 HIS 0.003 0.000 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00304 (37552) covalent geometry : angle 0.54345 (50728) hydrogen bonds : bond 0.03687 ( 2006) hydrogen bonds : angle 3.97655 ( 5913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: A 244 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8543 (mmt180) REVERT: A 656 ILE cc_start: 0.6956 (mt) cc_final: 0.6592 (tt) REVERT: A 689 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5714 (mp0) REVERT: A 698 PHE cc_start: 0.5338 (OUTLIER) cc_final: 0.5026 (m-10) REVERT: B 580 LEU cc_start: 0.8233 (tp) cc_final: 0.7927 (mt) REVERT: C 127 ASP cc_start: 0.8124 (t0) cc_final: 0.7808 (t70) REVERT: C 131 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8158 (mtp85) REVERT: C 153 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7564 (m) REVERT: C 265 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6267 (mt) REVERT: C 592 PHE cc_start: 0.6268 (t80) cc_final: 0.5874 (t80) REVERT: D 76 LEU cc_start: 0.6865 (mm) cc_final: 0.5969 (pp) REVERT: D 101 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: E 259 PHE cc_start: 0.8549 (t80) cc_final: 0.8068 (t80) REVERT: E 349 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7900 (tt) REVERT: E 363 LYS cc_start: 0.7251 (mptt) cc_final: 0.7027 (pttm) REVERT: G 94 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5120 (mm-30) REVERT: G 108 VAL cc_start: 0.6196 (OUTLIER) cc_final: 0.5596 (p) REVERT: G 155 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7320 (pt0) REVERT: G 308 PHE cc_start: 0.7730 (t80) cc_final: 0.7324 (t80) REVERT: H 97 GLN cc_start: 0.7036 (tp40) cc_final: 0.6764 (mm-40) REVERT: H 100 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: H 372 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7072 (tp40) REVERT: H 565 PHE cc_start: 0.7835 (t80) cc_final: 0.7345 (t80) REVERT: H 579 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8068 (mm) REVERT: H 592 PHE cc_start: 0.7451 (t80) cc_final: 0.7248 (t80) outliers start: 76 outliers final: 32 residues processed: 412 average time/residue: 0.2347 time to fit residues: 157.4822 Evaluate side-chains 360 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 302 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 442 optimal weight: 3.9990 chunk 378 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 313 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 HIS ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.168334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110439 restraints weight = 56897.505| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.16 r_work: 0.3257 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 37552 Z= 0.262 Angle : 0.656 13.318 50728 Z= 0.328 Chirality : 0.042 0.161 5848 Planarity : 0.005 0.054 6536 Dihedral : 4.522 22.118 5128 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.60 % Allowed : 13.85 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.33 (0.13), residues: 4624 helix: 0.40 (0.09), residues: 3208 sheet: -1.73 (0.39), residues: 160 loop : -1.41 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 249 TYR 0.015 0.002 TYR C 380 PHE 0.022 0.002 PHE G 565 TRP 0.025 0.002 TRP F 662 HIS 0.005 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00642 (37552) covalent geometry : angle 0.65650 (50728) hydrogen bonds : bond 0.04952 ( 2006) hydrogen bonds : angle 4.33822 ( 5913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 342 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 308 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6515 (t80) REVERT: A 656 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6574 (tt) REVERT: A 689 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: A 698 PHE cc_start: 0.5671 (OUTLIER) cc_final: 0.5352 (m-10) REVERT: B 494 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8916 (mp) REVERT: B 580 LEU cc_start: 0.8400 (tp) cc_final: 0.8093 (mt) REVERT: B 596 GLU cc_start: 0.6873 (mm-30) cc_final: 0.5943 (mm-30) REVERT: C 127 ASP cc_start: 0.8110 (t0) cc_final: 0.7870 (t70) REVERT: C 153 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (m) REVERT: C 592 PHE cc_start: 0.6432 (t80) cc_final: 0.6208 (t80) REVERT: C 685 HIS cc_start: 0.6869 (m-70) cc_final: 0.6565 (m-70) REVERT: D 149 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7157 (tp30) REVERT: D 235 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 325 ASP cc_start: 0.7750 (t0) cc_final: 0.7403 (p0) REVERT: E 349 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8102 (tt) REVERT: E 363 LYS cc_start: 0.7364 (mptt) cc_final: 0.7115 (pttm) REVERT: F 103 TRP cc_start: 0.6130 (t-100) cc_final: 0.5930 (t60) REVERT: G 108 VAL cc_start: 0.6276 (OUTLIER) cc_final: 0.5652 (p) REVERT: G 155 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7486 (pt0) REVERT: G 399 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6890 (mp0) REVERT: H 100 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: H 252 GLU cc_start: 0.8643 (tp30) cc_final: 0.8441 (tp30) REVERT: H 308 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7805 (t80) REVERT: H 372 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7169 (tp40) REVERT: H 565 PHE cc_start: 0.7948 (t80) cc_final: 0.7365 (t80) REVERT: H 579 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8138 (mm) outliers start: 102 outliers final: 52 residues processed: 420 average time/residue: 0.2298 time to fit residues: 156.6245 Evaluate side-chains 376 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 310 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 571 ASN Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 308 PHE Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 400 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 332 optimal weight: 0.7980 chunk 406 optimal weight: 20.0000 chunk 459 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 264 optimal weight: 0.0050 chunk 148 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.173003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116261 restraints weight = 56758.821| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.24 r_work: 0.3338 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37552 Z= 0.104 Angle : 0.543 13.605 50728 Z= 0.268 Chirality : 0.037 0.178 5848 Planarity : 0.004 0.053 6536 Dihedral : 4.071 21.649 5128 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 15.05 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.13), residues: 4624 helix: 0.77 (0.10), residues: 3216 sheet: -1.58 (0.40), residues: 160 loop : -1.17 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 249 TYR 0.009 0.001 TYR E 213 PHE 0.034 0.001 PHE E 96 TRP 0.028 0.001 TRP F 662 HIS 0.005 0.000 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00236 (37552) covalent geometry : angle 0.54292 (50728) hydrogen bonds : bond 0.03252 ( 2006) hydrogen bonds : angle 3.87998 ( 5913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 371 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: A 244 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8603 (mmt180) REVERT: A 308 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 656 ILE cc_start: 0.6947 (mt) cc_final: 0.6602 (tt) REVERT: A 689 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5756 (mp0) REVERT: A 698 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5424 (m-10) REVERT: B 196 GLU cc_start: 0.8709 (mp0) cc_final: 0.8419 (mp0) REVERT: B 376 ARG cc_start: 0.8396 (ttm110) cc_final: 0.8188 (ttm-80) REVERT: B 580 LEU cc_start: 0.8279 (tp) cc_final: 0.7998 (mt) REVERT: B 596 GLU cc_start: 0.6838 (mm-30) cc_final: 0.5893 (mm-30) REVERT: C 80 LYS cc_start: 0.5864 (mppt) cc_final: 0.5649 (ttpt) REVERT: C 127 ASP cc_start: 0.8118 (t0) cc_final: 0.7903 (t70) REVERT: C 153 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7432 (m) REVERT: C 592 PHE cc_start: 0.6131 (t80) cc_final: 0.5819 (t80) REVERT: C 609 GLN cc_start: 0.8365 (mp10) cc_final: 0.8060 (mp10) REVERT: D 76 LEU cc_start: 0.6883 (mm) cc_final: 0.5981 (pp) REVERT: D 173 LYS cc_start: 0.8394 (mtmm) cc_final: 0.8123 (tptp) REVERT: D 592 PHE cc_start: 0.7083 (t80) cc_final: 0.6609 (t80) REVERT: D 656 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6643 (pt) REVERT: E 134 GLN cc_start: 0.8285 (mp10) cc_final: 0.7802 (mt0) REVERT: E 349 LEU cc_start: 0.8153 (tp) cc_final: 0.7911 (tt) REVERT: E 363 LYS cc_start: 0.7255 (mptt) cc_final: 0.7042 (pttm) REVERT: E 687 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: F 74 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7812 (pm20) REVERT: G 108 VAL cc_start: 0.6242 (OUTLIER) cc_final: 0.5624 (p) REVERT: G 155 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7378 (pt0) REVERT: G 249 ARG cc_start: 0.7599 (mmm160) cc_final: 0.6961 (mmm-85) REVERT: G 259 PHE cc_start: 0.8261 (t80) cc_final: 0.7989 (t80) REVERT: G 308 PHE cc_start: 0.7769 (t80) cc_final: 0.7488 (t80) REVERT: G 327 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8244 (mt) REVERT: H 174 GLU cc_start: 0.7054 (tp30) cc_final: 0.6824 (tp30) REVERT: H 565 PHE cc_start: 0.7751 (t80) cc_final: 0.7185 (t80) REVERT: H 579 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8089 (mm) outliers start: 76 outliers final: 37 residues processed: 423 average time/residue: 0.2345 time to fit residues: 160.8166 Evaluate side-chains 380 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 333 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 687 TYR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 469 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 457 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 380 optimal weight: 0.0670 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 421 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114751 restraints weight = 57055.902| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.19 r_work: 0.3327 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37552 Z= 0.126 Angle : 0.553 16.482 50728 Z= 0.272 Chirality : 0.038 0.171 5848 Planarity : 0.004 0.053 6536 Dihedral : 3.994 21.503 5128 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.81 % Allowed : 15.84 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.13), residues: 4624 helix: 0.85 (0.10), residues: 3216 sheet: -1.46 (0.41), residues: 160 loop : -1.15 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 182 TYR 0.009 0.001 TYR E 213 PHE 0.030 0.001 PHE E 96 TRP 0.029 0.001 TRP F 662 HIS 0.003 0.000 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00302 (37552) covalent geometry : angle 0.55309 (50728) hydrogen bonds : bond 0.03541 ( 2006) hydrogen bonds : angle 3.86293 ( 5913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 343 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: A 146 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7920 (ttt-90) REVERT: A 244 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8543 (mmt180) REVERT: A 656 ILE cc_start: 0.6927 (mt) cc_final: 0.6570 (tt) REVERT: A 689 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5770 (mp0) REVERT: A 698 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5661 (m-10) REVERT: B 196 GLU cc_start: 0.8679 (mp0) cc_final: 0.8369 (mp0) REVERT: B 580 LEU cc_start: 0.8293 (tp) cc_final: 0.8019 (mt) REVERT: B 596 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6007 (mm-30) REVERT: C 80 LYS cc_start: 0.5854 (mppt) cc_final: 0.5616 (ttpt) REVERT: C 127 ASP cc_start: 0.8123 (t0) cc_final: 0.7887 (t70) REVERT: C 153 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7526 (m) REVERT: C 592 PHE cc_start: 0.6171 (t80) cc_final: 0.5897 (t80) REVERT: C 609 GLN cc_start: 0.8383 (mp10) cc_final: 0.8053 (mp10) REVERT: D 76 LEU cc_start: 0.6892 (mm) cc_final: 0.5935 (pp) REVERT: D 149 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6550 (tp30) REVERT: D 173 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8090 (tptp) REVERT: D 592 PHE cc_start: 0.7080 (t80) cc_final: 0.6509 (t80) REVERT: D 656 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6555 (pt) REVERT: E 155 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6855 (mm-30) REVERT: E 349 LEU cc_start: 0.8149 (tp) cc_final: 0.7892 (tt) REVERT: E 363 LYS cc_start: 0.7266 (mptt) cc_final: 0.7043 (pttm) REVERT: E 687 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: G 108 VAL cc_start: 0.6207 (OUTLIER) cc_final: 0.5596 (p) REVERT: G 155 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7400 (pt0) REVERT: G 259 PHE cc_start: 0.8240 (t80) cc_final: 0.7949 (t80) REVERT: G 308 PHE cc_start: 0.7773 (t80) cc_final: 0.7490 (t80) REVERT: G 394 LEU cc_start: 0.9038 (mp) cc_final: 0.8813 (mp) REVERT: H 100 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: H 174 GLU cc_start: 0.7093 (tp30) cc_final: 0.6860 (tp30) REVERT: H 372 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7089 (tp40) REVERT: H 565 PHE cc_start: 0.7786 (t80) cc_final: 0.7295 (t80) REVERT: H 579 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8143 (mm) outliers start: 71 outliers final: 48 residues processed: 391 average time/residue: 0.2317 time to fit residues: 146.9694 Evaluate side-chains 384 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 326 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 687 TYR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 295 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 470 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 221 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 688 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.167438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109133 restraints weight = 57044.611| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.44 r_work: 0.3226 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 37552 Z= 0.303 Angle : 0.684 15.550 50728 Z= 0.342 Chirality : 0.044 0.203 5848 Planarity : 0.005 0.054 6536 Dihedral : 4.526 22.704 5128 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.13), residues: 4624 helix: 0.45 (0.09), residues: 3208 sheet: -1.55 (0.40), residues: 160 loop : -1.37 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 249 TYR 0.014 0.002 TYR C 380 PHE 0.024 0.002 PHE B 347 TRP 0.025 0.002 TRP F 662 HIS 0.005 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00744 (37552) covalent geometry : angle 0.68392 (50728) hydrogen bonds : bond 0.05023 ( 2006) hydrogen bonds : angle 4.37747 ( 5913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 323 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: A 308 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6409 (t80) REVERT: A 656 ILE cc_start: 0.6634 (mt) cc_final: 0.6340 (tt) REVERT: A 689 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: B 580 LEU cc_start: 0.8268 (tp) cc_final: 0.7983 (mt) REVERT: B 596 GLU cc_start: 0.6951 (mm-30) cc_final: 0.5895 (mm-30) REVERT: C 80 LYS cc_start: 0.5838 (mppt) cc_final: 0.5629 (ttpt) REVERT: C 127 ASP cc_start: 0.8210 (t0) cc_final: 0.7962 (t70) REVERT: C 153 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7283 (m) REVERT: C 592 PHE cc_start: 0.6038 (t80) cc_final: 0.5780 (t80) REVERT: C 685 HIS cc_start: 0.6872 (m-70) cc_final: 0.6579 (m-70) REVERT: D 149 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: D 165 LEU cc_start: 0.8803 (mm) cc_final: 0.8593 (mm) REVERT: D 173 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8061 (tptp) REVERT: E 134 GLN cc_start: 0.8383 (mp10) cc_final: 0.8133 (mt0) REVERT: E 325 ASP cc_start: 0.7475 (t0) cc_final: 0.7197 (p0) REVERT: E 349 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7750 (tt) REVERT: E 363 LYS cc_start: 0.7223 (mptt) cc_final: 0.6994 (pttm) REVERT: E 687 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: F 244 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8004 (tpt170) REVERT: G 155 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7422 (pt0) REVERT: G 457 MET cc_start: 0.9505 (mtt) cc_final: 0.9246 (mtt) REVERT: H 372 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6792 (tp40) REVERT: H 579 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7932 (mm) outliers start: 94 outliers final: 57 residues processed: 391 average time/residue: 0.2296 time to fit residues: 146.2678 Evaluate side-chains 377 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 312 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 687 TYR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 110 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN B 571 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.169812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112197 restraints weight = 56911.921| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.18 r_work: 0.3292 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37552 Z= 0.165 Angle : 0.601 16.642 50728 Z= 0.295 Chirality : 0.039 0.208 5848 Planarity : 0.004 0.054 6536 Dihedral : 4.281 22.038 5128 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.96 % Allowed : 16.35 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.13), residues: 4624 helix: 0.62 (0.10), residues: 3216 sheet: -1.47 (0.41), residues: 160 loop : -1.27 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 249 TYR 0.010 0.001 TYR E 213 PHE 0.027 0.001 PHE E 96 TRP 0.025 0.001 TRP F 662 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00401 (37552) covalent geometry : angle 0.60075 (50728) hydrogen bonds : bond 0.03998 ( 2006) hydrogen bonds : angle 4.09725 ( 5913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 335 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: A 244 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8514 (mmt180) REVERT: A 308 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.6408 (t80) REVERT: A 656 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6387 (tt) REVERT: A 689 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: B 196 GLU cc_start: 0.8572 (mp0) cc_final: 0.8283 (mp0) REVERT: B 376 ARG cc_start: 0.8290 (ttm110) cc_final: 0.8029 (ttm-80) REVERT: B 580 LEU cc_start: 0.8212 (tp) cc_final: 0.7939 (mt) REVERT: B 596 GLU cc_start: 0.7040 (mm-30) cc_final: 0.5980 (mm-30) REVERT: C 127 ASP cc_start: 0.8175 (t0) cc_final: 0.7928 (t70) REVERT: C 153 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7251 (m) REVERT: C 592 PHE cc_start: 0.6174 (t80) cc_final: 0.5671 (t80) REVERT: C 685 HIS cc_start: 0.6758 (m-70) cc_final: 0.6477 (m-70) REVERT: D 149 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6951 (tp30) REVERT: D 165 LEU cc_start: 0.8752 (mm) cc_final: 0.8511 (mm) REVERT: D 173 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8127 (tptp) REVERT: D 592 PHE cc_start: 0.7102 (t80) cc_final: 0.6599 (t80) REVERT: E 325 ASP cc_start: 0.7431 (t0) cc_final: 0.7197 (p0) REVERT: E 349 LEU cc_start: 0.8000 (tp) cc_final: 0.7771 (tt) REVERT: E 363 LYS cc_start: 0.7198 (mptt) cc_final: 0.6971 (pttm) REVERT: E 687 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: G 155 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7439 (pt0) REVERT: G 259 PHE cc_start: 0.8134 (t80) cc_final: 0.7846 (t80) REVERT: G 565 PHE cc_start: 0.7113 (t80) cc_final: 0.6756 (t80) REVERT: H 565 PHE cc_start: 0.7623 (t80) cc_final: 0.7087 (t80) REVERT: H 575 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6341 (tp40) REVERT: H 579 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7934 (mm) outliers start: 77 outliers final: 55 residues processed: 388 average time/residue: 0.2357 time to fit residues: 148.4695 Evaluate side-chains 380 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 317 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 687 TYR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 18 optimal weight: 0.0970 chunk 461 optimal weight: 9.9990 chunk 366 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 378 optimal weight: 0.9980 chunk 331 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115250 restraints weight = 56809.756| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.15 r_work: 0.3324 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37552 Z= 0.117 Angle : 0.570 16.885 50728 Z= 0.278 Chirality : 0.038 0.219 5848 Planarity : 0.004 0.054 6536 Dihedral : 4.042 21.887 5128 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.79 % Allowed : 16.66 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.13), residues: 4624 helix: 0.84 (0.10), residues: 3216 sheet: -1.42 (0.41), residues: 160 loop : -1.18 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 249 TYR 0.009 0.001 TYR E 213 PHE 0.018 0.001 PHE E 259 TRP 0.025 0.001 TRP F 662 HIS 0.003 0.000 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00279 (37552) covalent geometry : angle 0.56952 (50728) hydrogen bonds : bond 0.03400 ( 2006) hydrogen bonds : angle 3.90103 ( 5913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 350 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8595 (mmt180) REVERT: A 308 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.6408 (t80) REVERT: A 656 ILE cc_start: 0.6749 (mt) cc_final: 0.6425 (tt) REVERT: A 689 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5815 (mp0) REVERT: B 196 GLU cc_start: 0.8648 (mp0) cc_final: 0.8354 (mp0) REVERT: B 376 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8146 (ttm-80) REVERT: B 580 LEU cc_start: 0.8342 (tp) cc_final: 0.8093 (mt) REVERT: B 596 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6019 (mm-30) REVERT: C 127 ASP cc_start: 0.8202 (t0) cc_final: 0.7946 (t70) REVERT: C 153 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7393 (m) REVERT: C 592 PHE cc_start: 0.6180 (t80) cc_final: 0.5976 (t80) REVERT: D 94 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: D 149 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: D 165 LEU cc_start: 0.8798 (mm) cc_final: 0.8566 (mm) REVERT: D 173 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8128 (tptp) REVERT: D 592 PHE cc_start: 0.7127 (t80) cc_final: 0.6666 (t80) REVERT: E 155 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6841 (mm-30) REVERT: E 259 PHE cc_start: 0.8577 (t80) cc_final: 0.8239 (t80) REVERT: E 349 LEU cc_start: 0.8159 (tp) cc_final: 0.7908 (tt) REVERT: E 687 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: G 108 VAL cc_start: 0.6159 (OUTLIER) cc_final: 0.5555 (p) REVERT: G 155 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7395 (pt0) REVERT: G 249 ARG cc_start: 0.7518 (mmm160) cc_final: 0.6954 (mmm-85) REVERT: G 259 PHE cc_start: 0.8239 (t80) cc_final: 0.8016 (t80) REVERT: G 327 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8342 (mt) REVERT: G 565 PHE cc_start: 0.7037 (t80) cc_final: 0.6698 (t80) REVERT: H 565 PHE cc_start: 0.7716 (t80) cc_final: 0.7177 (t80) REVERT: H 579 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8068 (mm) outliers start: 70 outliers final: 56 residues processed: 399 average time/residue: 0.2280 time to fit residues: 149.1164 Evaluate side-chains 395 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 687 TYR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 685 HIS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 681 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 124 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 450 optimal weight: 0.7980 chunk 455 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 309 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 chunk 437 optimal weight: 9.9990 chunk 387 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN E 337 ASN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.171692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114821 restraints weight = 56887.237| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.13 r_work: 0.3329 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37552 Z= 0.124 Angle : 0.576 16.701 50728 Z= 0.281 Chirality : 0.038 0.224 5848 Planarity : 0.004 0.054 6536 Dihedral : 3.986 22.719 5128 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.89 % Allowed : 16.81 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.13), residues: 4624 helix: 0.88 (0.10), residues: 3216 sheet: -1.39 (0.41), residues: 160 loop : -1.14 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 249 TYR 0.009 0.001 TYR E 213 PHE 0.026 0.001 PHE E 96 TRP 0.026 0.001 TRP F 662 HIS 0.003 0.000 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00299 (37552) covalent geometry : angle 0.57648 (50728) hydrogen bonds : bond 0.03497 ( 2006) hydrogen bonds : angle 3.88693 ( 5913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12937.07 seconds wall clock time: 221 minutes 22.72 seconds (13282.72 seconds total)