Starting phenix.real_space_refine on Mon Jun 16 23:33:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tdo_25837/06_2025/7tdo_25837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tdo_25837/06_2025/7tdo_25837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tdo_25837/06_2025/7tdo_25837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tdo_25837/06_2025/7tdo_25837.map" model { file = "/net/cci-nas-00/data/ceres_data/7tdo_25837/06_2025/7tdo_25837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tdo_25837/06_2025/7tdo_25837.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.111 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 12348 2.51 5 N 3420 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19572 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.45, per 1000 atoms: 0.43 Number of scatterers: 19572 At special positions: 0 Unit cell: (135.472, 140.945, 90.3144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3732 8.00 N 3420 7.00 C 12348 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: 5.08 Conformation dependent library (CDL) restraints added in 2.7 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 49.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.678A pdb=" N LEU A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 252 removed outlier: 3.576A pdb=" N ALA A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 4.428A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.879A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.700A pdb=" N LYS A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.732A pdb=" N ILE A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.014A pdb=" N LEU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.700A pdb=" N PHE A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 removed outlier: 3.936A pdb=" N ILE A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 431 " --> pdb=" O HIS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.597A pdb=" N ALA A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 480' Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.792A pdb=" N VAL A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 575 removed outlier: 3.559A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 587 removed outlier: 4.215A pdb=" N ASN A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 602 removed outlier: 3.553A pdb=" N SER A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.677A pdb=" N LEU B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 252 removed outlier: 3.577A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 266 removed outlier: 4.427A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.879A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 332 through 344 removed outlier: 3.700A pdb=" N LYS B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.732A pdb=" N ILE B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 385 removed outlier: 4.014A pdb=" N LEU B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.701A pdb=" N PHE B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 434 removed outlier: 3.936A pdb=" N ILE B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS B 427 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 431 " --> pdb=" O HIS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.598A pdb=" N ALA B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 480' Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.792A pdb=" N VAL B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 575 removed outlier: 3.558A pdb=" N ALA B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 559 " --> pdb=" O GLU B 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 587 removed outlier: 4.215A pdb=" N ASN B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 602 removed outlier: 3.552A pdb=" N SER B 602 " --> pdb=" O ARG B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 206 through 218 removed outlier: 3.678A pdb=" N LEU C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 252 removed outlier: 3.576A pdb=" N ALA C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 removed outlier: 4.427A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 294 removed outlier: 3.879A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 332 through 344 removed outlier: 3.700A pdb=" N LYS C 337 " --> pdb=" O MET C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.732A pdb=" N ILE C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 385 removed outlier: 4.014A pdb=" N LEU C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.700A pdb=" N PHE C 394 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 removed outlier: 3.936A pdb=" N ILE C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 427 " --> pdb=" O TYR C 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 431 " --> pdb=" O HIS C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.597A pdb=" N ALA C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 480' Processing helix chain 'C' and resid 482 through 490 removed outlier: 3.792A pdb=" N VAL C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 575 removed outlier: 3.558A pdb=" N ALA C 550 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 552 " --> pdb=" O GLU C 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU C 555 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 556 " --> pdb=" O LYS C 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 559 " --> pdb=" O GLU C 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 587 removed outlier: 4.215A pdb=" N ASN C 581 " --> pdb=" O LYS C 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 removed outlier: 3.553A pdb=" N SER C 602 " --> pdb=" O ARG C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 206 through 218 removed outlier: 3.677A pdb=" N LEU D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 252 removed outlier: 3.577A pdb=" N ALA D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS D 252 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 removed outlier: 4.428A pdb=" N VAL D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 3.879A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.700A pdb=" N LYS D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.732A pdb=" N ILE D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 4.014A pdb=" N LEU D 370 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 403 removed outlier: 3.700A pdb=" N PHE D 394 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 434 removed outlier: 3.936A pdb=" N ILE D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 427 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 431 " --> pdb=" O HIS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 480 removed outlier: 3.598A pdb=" N ALA D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 480' Processing helix chain 'D' and resid 482 through 490 removed outlier: 3.792A pdb=" N VAL D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 575 removed outlier: 3.558A pdb=" N ALA D 550 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 552 " --> pdb=" O GLU D 548 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU D 555 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 556 " --> pdb=" O LYS D 552 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 559 " --> pdb=" O GLU D 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 587 removed outlier: 4.215A pdb=" N ASN D 581 " --> pdb=" O LYS D 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 602 removed outlier: 3.553A pdb=" N SER D 602 " --> pdb=" O ARG D 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 180 Processing helix chain 'E' and resid 206 through 218 removed outlier: 3.677A pdb=" N LEU E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA E 218 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 252 removed outlier: 3.576A pdb=" N ALA E 251 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS E 252 " --> pdb=" O GLN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 266 removed outlier: 4.427A pdb=" N VAL E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 294 removed outlier: 3.880A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 318 Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.700A pdb=" N LYS E 337 " --> pdb=" O MET E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 3.732A pdb=" N ILE E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 4.014A pdb=" N LEU E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU E 371 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 403 removed outlier: 3.700A pdb=" N PHE E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 400 " --> pdb=" O GLU E 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 434 removed outlier: 3.936A pdb=" N ILE E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS E 427 " --> pdb=" O TYR E 423 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 428 " --> pdb=" O GLU E 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 431 " --> pdb=" O HIS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 480 removed outlier: 3.598A pdb=" N ALA E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 474 through 480' Processing helix chain 'E' and resid 482 through 490 removed outlier: 3.792A pdb=" N VAL E 488 " --> pdb=" O ALA E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 575 removed outlier: 3.558A pdb=" N ALA E 550 " --> pdb=" O SER E 546 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 552 " --> pdb=" O GLU E 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU E 555 " --> pdb=" O SER E 551 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 556 " --> pdb=" O LYS E 552 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 559 " --> pdb=" O GLU E 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 562 " --> pdb=" O LYS E 558 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 569 " --> pdb=" O TYR E 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 574 " --> pdb=" O GLU E 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR E 575 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 587 removed outlier: 4.216A pdb=" N ASN E 581 " --> pdb=" O LYS E 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 602 removed outlier: 3.553A pdb=" N SER E 602 " --> pdb=" O ARG E 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 180 Processing helix chain 'F' and resid 206 through 218 removed outlier: 3.678A pdb=" N LEU F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 252 removed outlier: 3.576A pdb=" N ALA F 251 " --> pdb=" O ALA F 247 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS F 252 " --> pdb=" O GLN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 266 removed outlier: 4.427A pdb=" N VAL F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 294 removed outlier: 3.879A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 332 through 344 removed outlier: 3.700A pdb=" N LYS F 337 " --> pdb=" O MET F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 removed outlier: 3.732A pdb=" N ILE F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 385 removed outlier: 4.014A pdb=" N LEU F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY F 385 " --> pdb=" O ALA F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 403 removed outlier: 3.701A pdb=" N PHE F 394 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 434 removed outlier: 3.936A pdb=" N ILE F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS F 427 " --> pdb=" O TYR F 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 428 " --> pdb=" O GLU F 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER F 431 " --> pdb=" O HIS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 480 removed outlier: 3.598A pdb=" N ALA F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 480 " --> pdb=" O LEU F 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 474 through 480' Processing helix chain 'F' and resid 482 through 490 removed outlier: 3.792A pdb=" N VAL F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 575 removed outlier: 3.559A pdb=" N ALA F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 552 " --> pdb=" O GLU F 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 555 " --> pdb=" O SER F 551 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 556 " --> pdb=" O LYS F 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR F 562 " --> pdb=" O LYS F 558 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 569 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 570 " --> pdb=" O GLU F 566 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS F 574 " --> pdb=" O GLU F 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 575 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 587 removed outlier: 4.215A pdb=" N ASN F 581 " --> pdb=" O LYS F 577 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 602 removed outlier: 3.553A pdb=" N SER F 602 " --> pdb=" O ARG F 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.422A pdb=" N PHE A 223 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP A 260 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A 225 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 301 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 324 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 458 removed outlier: 7.386A pdb=" N TYR A 455 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 443 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 457 " --> pdb=" O HIS A 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.422A pdb=" N PHE B 223 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP B 260 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 225 " --> pdb=" O ASP B 260 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 301 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 324 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 455 through 458 removed outlier: 7.386A pdb=" N TYR B 455 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 443 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 457 " --> pdb=" O HIS B 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.422A pdb=" N PHE C 223 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP C 260 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE C 225 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 301 " --> pdb=" O CYS C 255 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS C 324 " --> pdb=" O GLY C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 455 through 458 removed outlier: 7.386A pdb=" N TYR C 455 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE C 443 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 457 " --> pdb=" O HIS C 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 222 through 226 removed outlier: 6.422A pdb=" N PHE D 223 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP D 260 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE D 225 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 301 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS D 324 " --> pdb=" O GLY D 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 455 through 458 removed outlier: 7.386A pdb=" N TYR D 455 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE D 443 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU D 457 " --> pdb=" O HIS D 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 222 through 226 removed outlier: 6.422A pdb=" N PHE E 223 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP E 260 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE E 225 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 301 " --> pdb=" O CYS E 255 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS E 324 " --> pdb=" O GLY E 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 455 through 458 removed outlier: 7.386A pdb=" N TYR E 455 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE E 443 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU E 457 " --> pdb=" O HIS E 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 222 through 226 removed outlier: 6.422A pdb=" N PHE F 223 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP F 260 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE F 225 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE F 301 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS F 324 " --> pdb=" O GLY F 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 455 through 458 removed outlier: 7.385A pdb=" N TYR F 455 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE F 443 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU F 457 " --> pdb=" O HIS F 441 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1944 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: 6.00 Time building geometry restraints manager: 5.91 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: 6663 1.34 - 1.46: 2226 1.46 - 1.57: 10851 1.57 - 1.69: 18 1.69 - 1.80: 102 Bond restraints: 19860 Sorted by residual: bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.366 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C4 ADP D 701 " pdb=" C5 ADP D 701 " ideal model delta sigma weight residual 1.490 1.366 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C4 ADP E 701 " pdb=" C5 ADP E 701 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 26192 1.44 - 2.88: 500 2.88 - 4.31: 96 4.31 - 5.75: 44 5.75 - 7.19: 18 Bond angle restraints: 26850 Sorted by residual: angle pdb=" CA LEU D 173 " pdb=" CB LEU D 173 " pdb=" CG LEU D 173 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.22e+00 angle pdb=" CA LEU A 173 " pdb=" CB LEU A 173 " pdb=" CG LEU A 173 " ideal model delta sigma weight residual 116.30 123.47 -7.17 3.50e+00 8.16e-02 4.20e+00 angle pdb=" CA LEU C 173 " pdb=" CB LEU C 173 " pdb=" CG LEU C 173 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" O1B ADP C 701 " pdb=" PB ADP C 701 " pdb=" O3B ADP C 701 " ideal model delta sigma weight residual 119.90 113.78 6.12 3.00e+00 1.11e-01 4.16e+00 angle pdb=" CA LEU E 173 " pdb=" CB LEU E 173 " pdb=" CG LEU E 173 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.16e+00 ... (remaining 26845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.67: 11960 31.67 - 63.35: 256 63.35 - 95.02: 12 95.02 - 126.69: 12 126.69 - 158.37: 6 Dihedral angle restraints: 12246 sinusoidal: 5046 harmonic: 7200 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual 300.00 141.64 158.37 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP D 701 " pdb=" O5' ADP D 701 " pdb=" PA ADP D 701 " pdb=" O2A ADP D 701 " ideal model delta sinusoidal sigma weight residual 300.00 141.68 158.33 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP E 701 " pdb=" O5' ADP E 701 " pdb=" PA ADP E 701 " pdb=" O2A ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 141.68 158.33 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1884 0.033 - 0.067: 902 0.067 - 0.100: 189 0.100 - 0.133: 121 0.133 - 0.167: 6 Chirality restraints: 3102 Sorted by residual: chirality pdb=" CB THR D 362 " pdb=" CA THR D 362 " pdb=" OG1 THR D 362 " pdb=" CG2 THR D 362 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CB THR C 362 " pdb=" CA THR C 362 " pdb=" OG1 THR C 362 " pdb=" CG2 THR C 362 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB THR A 362 " pdb=" CA THR A 362 " pdb=" OG1 THR A 362 " pdb=" CG2 THR A 362 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 3099 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 201 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 202 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 202 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 202 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 201 " -0.033 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO D 202 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 202 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 202 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 201 " 0.033 5.00e-02 4.00e+02 5.13e-02 4.20e+00 pdb=" N PRO B 202 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.028 5.00e-02 4.00e+02 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5280 2.81 - 3.33: 17054 3.33 - 3.85: 27362 3.85 - 4.38: 32506 4.38 - 4.90: 55815 Nonbonded interactions: 138017 Sorted by model distance: nonbonded pdb=" OG SER E 226 " pdb=" OG SER E 228 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 226 " pdb=" OG SER A 228 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 226 " pdb=" OG SER D 228 " model vdw 2.285 3.040 nonbonded pdb=" OG SER B 226 " pdb=" OG SER B 228 " model vdw 2.285 3.040 nonbonded pdb=" OG SER F 226 " pdb=" OG SER F 228 " model vdw 2.285 3.040 ... (remaining 138012 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 40.740 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 19860 Z= 0.196 Angle : 0.574 7.189 26850 Z= 0.302 Chirality : 0.043 0.167 3102 Planarity : 0.004 0.051 3492 Dihedral : 14.508 158.368 7590 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2484 helix: -1.16 (0.15), residues: 1170 sheet: 1.59 (0.35), residues: 198 loop : -0.59 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 526 HIS 0.003 0.001 HIS C 458 PHE 0.004 0.001 PHE E 223 TYR 0.009 0.001 TYR D 545 ARG 0.002 0.000 ARG D 576 Details of bonding type rmsd hydrogen bonds : bond 0.28016 ( 678) hydrogen bonds : angle 7.28411 ( 1944) covalent geometry : bond 0.00413 (19860) covalent geometry : angle 0.57360 (26850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4400 time to fit residues: 111.3705 Evaluate side-chains 109 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.0970 chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 0.0370 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.065893 restraints weight = 48615.740| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.27 r_work: 0.2735 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19860 Z= 0.144 Angle : 0.636 15.837 26850 Z= 0.308 Chirality : 0.043 0.145 3102 Planarity : 0.004 0.042 3492 Dihedral : 9.893 143.561 2778 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.20 % Allowed : 4.89 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2484 helix: -0.53 (0.15), residues: 1206 sheet: 1.73 (0.35), residues: 198 loop : -0.59 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 526 HIS 0.005 0.001 HIS A 252 PHE 0.044 0.001 PHE E 246 TYR 0.008 0.001 TYR B 545 ARG 0.006 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.05964 ( 678) hydrogen bonds : angle 4.86394 ( 1944) covalent geometry : bond 0.00313 (19860) covalent geometry : angle 0.63565 (26850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8477 (tpp) cc_final: 0.8089 (tpp) REVERT: A 308 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: A 333 MET cc_start: 0.8257 (tmm) cc_final: 0.8005 (tmm) REVERT: A 502 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B 291 MET cc_start: 0.8185 (ttt) cc_final: 0.7574 (ptm) REVERT: B 308 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8344 (tpm170) REVERT: B 310 ASP cc_start: 0.8101 (m-30) cc_final: 0.7832 (m-30) REVERT: B 376 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8832 (mm-30) REVERT: C 308 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7862 (mmm-85) REVERT: C 310 ASP cc_start: 0.8860 (t0) cc_final: 0.8597 (t0) REVERT: C 520 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7922 (tm-30) REVERT: D 318 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8520 (tpt170) REVERT: D 391 MET cc_start: 0.8120 (tpp) cc_final: 0.7818 (tpp) REVERT: D 519 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8025 (tm-30) outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 0.4119 time to fit residues: 71.9240 Evaluate side-chains 100 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 303 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 231 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 114 optimal weight: 0.0000 chunk 222 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 249 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 ASN D 514 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065403 restraints weight = 48268.705| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.27 r_work: 0.2725 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19860 Z= 0.114 Angle : 0.566 11.548 26850 Z= 0.268 Chirality : 0.042 0.155 3102 Planarity : 0.004 0.059 3492 Dihedral : 8.726 138.125 2778 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.15 % Allowed : 7.82 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2484 helix: -0.12 (0.15), residues: 1206 sheet: 2.01 (0.36), residues: 198 loop : -0.47 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 526 HIS 0.002 0.001 HIS E 458 PHE 0.039 0.001 PHE E 246 TYR 0.007 0.001 TYR B 423 ARG 0.010 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 678) hydrogen bonds : angle 4.22988 ( 1944) covalent geometry : bond 0.00251 (19860) covalent geometry : angle 0.56619 (26850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8480 (tpp) cc_final: 0.8072 (tpp) REVERT: A 502 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8241 (tm-30) REVERT: B 291 MET cc_start: 0.8295 (ttt) cc_final: 0.7791 (ptm) REVERT: B 308 ARG cc_start: 0.8710 (tpp-160) cc_final: 0.8361 (tpm170) REVERT: B 310 ASP cc_start: 0.8204 (m-30) cc_final: 0.7898 (m-30) REVERT: B 376 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8844 (mm-30) REVERT: C 187 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9104 (m110) REVERT: D 318 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8542 (tpt170) REVERT: D 391 MET cc_start: 0.8154 (tpp) cc_final: 0.7766 (tpp) REVERT: D 502 GLU cc_start: 0.9237 (tt0) cc_final: 0.8658 (tm-30) REVERT: E 308 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.7740 (tpm170) REVERT: F 260 ASP cc_start: 0.7937 (t0) cc_final: 0.7657 (p0) REVERT: F 318 ARG cc_start: 0.8719 (mmt180) cc_final: 0.8440 (mmt180) outliers start: 3 outliers final: 2 residues processed: 104 average time/residue: 0.5599 time to fit residues: 84.8630 Evaluate side-chains 99 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 316 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 121 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 HIS D 187 ASN ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS E 224 HIS F 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.062018 restraints weight = 49547.390| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 4.27 r_work: 0.2630 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19860 Z= 0.209 Angle : 0.612 9.582 26850 Z= 0.297 Chirality : 0.044 0.169 3102 Planarity : 0.004 0.036 3492 Dihedral : 7.941 128.046 2778 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.39 % Allowed : 9.78 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2484 helix: 0.02 (0.15), residues: 1212 sheet: 1.93 (0.35), residues: 198 loop : -0.60 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 526 HIS 0.007 0.002 HIS E 252 PHE 0.030 0.001 PHE E 246 TYR 0.008 0.001 TYR A 465 ARG 0.014 0.000 ARG C 188 Details of bonding type rmsd hydrogen bonds : bond 0.05512 ( 678) hydrogen bonds : angle 4.31301 ( 1944) covalent geometry : bond 0.00484 (19860) covalent geometry : angle 0.61201 (26850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 291 MET cc_start: 0.8250 (ttt) cc_final: 0.7740 (ptm) REVERT: B 308 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8241 (tpm170) REVERT: B 310 ASP cc_start: 0.8291 (m-30) cc_final: 0.7991 (m-30) REVERT: B 376 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8884 (mm-30) REVERT: B 502 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8813 (tm-30) REVERT: C 308 ARG cc_start: 0.8823 (tpp-160) cc_final: 0.8488 (tpm170) REVERT: C 310 ASP cc_start: 0.8782 (t0) cc_final: 0.8455 (t0) REVERT: D 391 MET cc_start: 0.8168 (tpp) cc_final: 0.7764 (tpp) REVERT: D 502 GLU cc_start: 0.9299 (tt0) cc_final: 0.8725 (tm-30) REVERT: D 520 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8520 (tm-30) REVERT: E 308 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: F 318 ARG cc_start: 0.8843 (mmt180) cc_final: 0.8439 (mmm160) REVERT: F 376 GLU cc_start: 0.9380 (tp30) cc_final: 0.9060 (tp30) outliers start: 8 outliers final: 3 residues processed: 105 average time/residue: 0.4283 time to fit residues: 64.2957 Evaluate side-chains 96 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 316 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 121 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 156 optimal weight: 0.0570 chunk 118 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.099515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.064852 restraints weight = 48827.780| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.24 r_work: 0.2693 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19860 Z= 0.096 Angle : 0.529 8.121 26850 Z= 0.249 Chirality : 0.041 0.140 3102 Planarity : 0.003 0.034 3492 Dihedral : 7.379 114.339 2778 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.39 % Allowed : 10.51 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2484 helix: 0.41 (0.15), residues: 1230 sheet: 2.14 (0.35), residues: 198 loop : -0.51 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 526 HIS 0.004 0.001 HIS E 252 PHE 0.019 0.001 PHE E 246 TYR 0.007 0.001 TYR C 545 ARG 0.013 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 678) hydrogen bonds : angle 3.67826 ( 1944) covalent geometry : bond 0.00205 (19860) covalent geometry : angle 0.52881 (26850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8608 (tpp) cc_final: 0.8254 (tpp) REVERT: A 502 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 291 MET cc_start: 0.8335 (ttt) cc_final: 0.7800 (ptm) REVERT: B 308 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8189 (tpm170) REVERT: B 310 ASP cc_start: 0.8283 (m-30) cc_final: 0.7975 (m-30) REVERT: B 376 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8835 (mm-30) REVERT: B 502 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8777 (tm-30) REVERT: B 514 GLN cc_start: 0.8465 (mt0) cc_final: 0.8029 (mp10) REVERT: C 308 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8188 (tpm170) REVERT: C 310 ASP cc_start: 0.8854 (t0) cc_final: 0.8572 (t0) REVERT: C 520 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8162 (tm-30) REVERT: D 520 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8544 (tm-30) REVERT: E 308 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8129 (mmm-85) REVERT: E 376 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8991 (mm-30) REVERT: F 318 ARG cc_start: 0.8577 (mmt180) cc_final: 0.8130 (mmm160) REVERT: F 376 GLU cc_start: 0.9359 (tp30) cc_final: 0.8978 (tp30) REVERT: F 514 GLN cc_start: 0.8349 (mt0) cc_final: 0.8027 (mp10) outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.5023 time to fit residues: 78.2475 Evaluate side-chains 99 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 192 optimal weight: 4.9990 chunk 217 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 187 ASN B 343 HIS C 343 HIS ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062686 restraints weight = 48976.570| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.14 r_work: 0.2690 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19860 Z= 0.142 Angle : 0.543 7.617 26850 Z= 0.256 Chirality : 0.042 0.133 3102 Planarity : 0.003 0.034 3492 Dihedral : 7.043 104.117 2778 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.68 % Allowed : 11.05 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2484 helix: 0.65 (0.16), residues: 1224 sheet: 2.08 (0.35), residues: 198 loop : -0.49 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 526 HIS 0.004 0.001 HIS D 427 PHE 0.018 0.001 PHE E 246 TYR 0.007 0.001 TYR F 545 ARG 0.008 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 678) hydrogen bonds : angle 3.71893 ( 1944) covalent geometry : bond 0.00333 (19860) covalent geometry : angle 0.54298 (26850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8614 (tpp) cc_final: 0.8290 (tpp) REVERT: A 502 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 291 MET cc_start: 0.8274 (ttt) cc_final: 0.7708 (ptm) REVERT: B 308 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8362 (tpp-160) REVERT: B 376 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8872 (mm-30) REVERT: B 502 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8953 (tm-30) REVERT: B 514 GLN cc_start: 0.8640 (mt0) cc_final: 0.8243 (mp10) REVERT: C 308 ARG cc_start: 0.8625 (tpp-160) cc_final: 0.8278 (tpm170) REVERT: C 310 ASP cc_start: 0.8811 (t0) cc_final: 0.8495 (t0) REVERT: C 520 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 502 GLU cc_start: 0.9344 (tt0) cc_final: 0.8762 (tm-30) REVERT: E 308 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8364 (mmm-85) REVERT: E 318 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7808 (mmp80) REVERT: F 318 ARG cc_start: 0.8812 (mmt180) cc_final: 0.8367 (mmm160) REVERT: F 376 GLU cc_start: 0.9379 (tp30) cc_final: 0.9000 (tp30) REVERT: F 514 GLN cc_start: 0.8509 (mt0) cc_final: 0.8210 (mp10) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 0.4172 time to fit residues: 65.3059 Evaluate side-chains 98 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 194 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 225 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS E 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.063776 restraints weight = 48824.446| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.20 r_work: 0.2717 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19860 Z= 0.100 Angle : 0.524 8.481 26850 Z= 0.244 Chirality : 0.041 0.134 3102 Planarity : 0.003 0.033 3492 Dihedral : 6.701 97.216 2778 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.64 % Allowed : 11.53 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2484 helix: 0.89 (0.15), residues: 1230 sheet: 2.19 (0.35), residues: 198 loop : -0.44 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 526 HIS 0.011 0.001 HIS E 224 PHE 0.015 0.001 PHE E 246 TYR 0.008 0.001 TYR C 545 ARG 0.008 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 678) hydrogen bonds : angle 3.47228 ( 1944) covalent geometry : bond 0.00231 (19860) covalent geometry : angle 0.52361 (26850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8592 (tpp) cc_final: 0.8259 (tpp) REVERT: A 308 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8095 (mtm-85) REVERT: A 502 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 291 MET cc_start: 0.8339 (ttt) cc_final: 0.7802 (ptm) REVERT: B 308 ARG cc_start: 0.8838 (tpp-160) cc_final: 0.8461 (tpm170) REVERT: B 376 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8861 (mm-30) REVERT: B 502 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8924 (tm-30) REVERT: B 514 GLN cc_start: 0.8576 (mt0) cc_final: 0.8143 (mp10) REVERT: C 308 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8378 (tpp-160) REVERT: C 310 ASP cc_start: 0.8920 (t0) cc_final: 0.8706 (t0) REVERT: C 520 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8241 (tm-30) REVERT: D 171 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: D 502 GLU cc_start: 0.9314 (tt0) cc_final: 0.8729 (tm-30) REVERT: E 308 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8354 (mmm-85) REVERT: E 318 ARG cc_start: 0.8058 (mmt-90) cc_final: 0.7792 (mmp80) REVERT: F 318 ARG cc_start: 0.8581 (mmt180) cc_final: 0.8157 (mmm160) REVERT: F 376 GLU cc_start: 0.9355 (tp30) cc_final: 0.8942 (tp30) REVERT: F 514 GLN cc_start: 0.8533 (mt0) cc_final: 0.8205 (mp10) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.4158 time to fit residues: 66.2423 Evaluate side-chains 103 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 224 HIS Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 195 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.063026 restraints weight = 49147.344| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 4.23 r_work: 0.2698 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19860 Z= 0.121 Angle : 0.533 8.353 26850 Z= 0.249 Chirality : 0.042 0.133 3102 Planarity : 0.003 0.034 3492 Dihedral : 6.576 92.867 2778 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.54 % Allowed : 11.93 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2484 helix: 1.12 (0.16), residues: 1206 sheet: 2.10 (0.35), residues: 198 loop : -0.43 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 526 HIS 0.013 0.001 HIS E 224 PHE 0.013 0.001 PHE E 246 TYR 0.007 0.001 TYR B 545 ARG 0.007 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 678) hydrogen bonds : angle 3.49637 ( 1944) covalent geometry : bond 0.00281 (19860) covalent geometry : angle 0.53319 (26850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8628 (tpp) cc_final: 0.8290 (tpp) REVERT: A 502 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8583 (tm-30) REVERT: B 291 MET cc_start: 0.8333 (ttt) cc_final: 0.7769 (ptm) REVERT: B 308 ARG cc_start: 0.8831 (tpp-160) cc_final: 0.8462 (tpm170) REVERT: B 376 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8859 (mm-30) REVERT: B 502 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8945 (tm-30) REVERT: B 514 GLN cc_start: 0.8578 (mt0) cc_final: 0.8145 (mp10) REVERT: C 308 ARG cc_start: 0.8645 (tpp-160) cc_final: 0.8344 (tpp-160) REVERT: C 310 ASP cc_start: 0.8937 (t0) cc_final: 0.8727 (t0) REVERT: C 520 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 171 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: D 502 GLU cc_start: 0.9325 (tt0) cc_final: 0.8738 (tm-30) REVERT: E 308 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: E 318 ARG cc_start: 0.8043 (mmt-90) cc_final: 0.7772 (mmp80) REVERT: F 318 ARG cc_start: 0.8777 (mmt180) cc_final: 0.8350 (mmm160) REVERT: F 376 GLU cc_start: 0.9354 (tp30) cc_final: 0.8940 (tp30) REVERT: F 514 GLN cc_start: 0.8542 (mt0) cc_final: 0.8218 (mp10) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.4466 time to fit residues: 68.8464 Evaluate side-chains 104 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 224 HIS Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.063969 restraints weight = 48878.462| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.19 r_work: 0.2721 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19860 Z= 0.091 Angle : 0.522 9.440 26850 Z= 0.243 Chirality : 0.041 0.134 3102 Planarity : 0.003 0.033 3492 Dihedral : 6.449 95.778 2778 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.44 % Allowed : 12.02 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2484 helix: 1.31 (0.16), residues: 1206 sheet: 2.14 (0.35), residues: 198 loop : -0.44 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 526 HIS 0.017 0.001 HIS E 224 PHE 0.012 0.001 PHE E 246 TYR 0.008 0.001 TYR C 545 ARG 0.005 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 678) hydrogen bonds : angle 3.33152 ( 1944) covalent geometry : bond 0.00205 (19860) covalent geometry : angle 0.52249 (26850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8593 (tpp) cc_final: 0.8260 (tpp) REVERT: A 308 ARG cc_start: 0.8326 (mtm110) cc_final: 0.8050 (mtm-85) REVERT: A 438 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8690 (pm20) REVERT: A 502 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8578 (tm-30) REVERT: B 291 MET cc_start: 0.8337 (ttt) cc_final: 0.7775 (ptm) REVERT: B 308 ARG cc_start: 0.8823 (tpp-160) cc_final: 0.8452 (tpm170) REVERT: B 376 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8852 (mm-30) REVERT: B 502 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8944 (tm-30) REVERT: B 514 GLN cc_start: 0.8571 (mt0) cc_final: 0.8150 (mp10) REVERT: C 308 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8332 (tpp-160) REVERT: C 310 ASP cc_start: 0.8937 (t0) cc_final: 0.8713 (t0) REVERT: D 502 GLU cc_start: 0.9291 (tt0) cc_final: 0.8703 (tm-30) REVERT: E 308 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8398 (mmm-85) REVERT: E 318 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7780 (mmp80) REVERT: F 318 ARG cc_start: 0.8581 (mmt180) cc_final: 0.8161 (mmm160) REVERT: F 376 GLU cc_start: 0.9306 (tp30) cc_final: 0.8880 (tp30) REVERT: F 514 GLN cc_start: 0.8516 (mt0) cc_final: 0.8198 (mp10) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.4111 time to fit residues: 61.9957 Evaluate side-chains 101 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 224 HIS Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 247 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 chunk 251 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 150 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS E 224 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.063263 restraints weight = 48352.685| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 4.18 r_work: 0.2726 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19860 Z= 0.091 Angle : 0.524 11.055 26850 Z= 0.242 Chirality : 0.041 0.133 3102 Planarity : 0.003 0.033 3492 Dihedral : 6.246 94.000 2778 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.54 % Allowed : 12.07 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2484 helix: 1.47 (0.16), residues: 1206 sheet: 2.13 (0.35), residues: 198 loop : -0.42 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 526 HIS 0.021 0.001 HIS E 224 PHE 0.012 0.001 PHE E 246 TYR 0.007 0.001 TYR C 545 ARG 0.005 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 678) hydrogen bonds : angle 3.26701 ( 1944) covalent geometry : bond 0.00211 (19860) covalent geometry : angle 0.52351 (26850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8582 (tpp) cc_final: 0.8254 (tpp) REVERT: A 308 ARG cc_start: 0.8314 (mtm110) cc_final: 0.8078 (mtm-85) REVERT: A 438 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: A 502 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8582 (tm-30) REVERT: B 291 MET cc_start: 0.8331 (ttt) cc_final: 0.7768 (ptm) REVERT: B 308 ARG cc_start: 0.8820 (tpp-160) cc_final: 0.8442 (tpm170) REVERT: B 376 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8854 (mm-30) REVERT: B 502 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8942 (tm-30) REVERT: B 514 GLN cc_start: 0.8570 (mt0) cc_final: 0.8152 (mp10) REVERT: C 308 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8333 (tpp-160) REVERT: C 310 ASP cc_start: 0.8932 (t0) cc_final: 0.8706 (t0) REVERT: D 502 GLU cc_start: 0.9282 (tt0) cc_final: 0.8693 (tm-30) REVERT: E 308 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8299 (mmm-85) REVERT: F 318 ARG cc_start: 0.8574 (mmt180) cc_final: 0.8166 (mmm160) REVERT: F 376 GLU cc_start: 0.9309 (tp30) cc_final: 0.8850 (tp30) REVERT: F 514 GLN cc_start: 0.8532 (mt0) cc_final: 0.8214 (mp10) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.4089 time to fit residues: 62.0701 Evaluate side-chains 102 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 224 HIS Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 92 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS ** E 252 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.097512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062383 restraints weight = 48485.580| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.24 r_work: 0.2698 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.142 Angle : 0.548 11.584 26850 Z= 0.257 Chirality : 0.042 0.163 3102 Planarity : 0.003 0.034 3492 Dihedral : 6.144 96.543 2778 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.44 % Allowed : 12.41 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2484 helix: 1.48 (0.15), residues: 1206 sheet: 2.03 (0.35), residues: 198 loop : -0.41 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 526 HIS 0.022 0.001 HIS E 224 PHE 0.012 0.001 PHE E 246 TYR 0.007 0.001 TYR F 545 ARG 0.008 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 678) hydrogen bonds : angle 3.45169 ( 1944) covalent geometry : bond 0.00335 (19860) covalent geometry : angle 0.54812 (26850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9983.33 seconds wall clock time: 176 minutes 0.37 seconds (10560.37 seconds total)