Starting phenix.real_space_refine on Sun Aug 24 10:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tdo_25837/08_2025/7tdo_25837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tdo_25837/08_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_25837/08_2025/7tdo_25837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tdo_25837/08_2025/7tdo_25837.map" model { file = "/net/cci-nas-00/data/ceres_data/7tdo_25837/08_2025/7tdo_25837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tdo_25837/08_2025/7tdo_25837.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'TYR: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: B, C, D, E, F Time building chain proxies: 2.94, per 1000 atoms: 0.15 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: 1.68 Conformation dependent library (CDL) restraints added in 699.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 2.66 Time building geometry restraints manager: 2.22 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.980 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- 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 : 4.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG D 576 TYR 0.009 0.001 TYR D 545 PHE 0.004 0.001 PHE E 223 TRP 0.006 0.001 TRP C 526 HIS 0.003 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00413 (19860) covalent geometry : angle 0.57360 (26850) hydrogen bonds : bond 0.28016 ( 678) hydrogen bonds : angle 7.28411 ( 1944) *********************** 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 : 0.813 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: 0.1741 time to fit residues: 42.8965 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.100712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065523 restraints weight = 48899.171| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.30 r_work: 0.2724 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.160 Angle : 0.634 15.189 26850 Z= 0.311 Chirality : 0.043 0.147 3102 Planarity : 0.004 0.042 3492 Dihedral : 9.980 144.843 2778 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.17), residues: 2484 helix: -0.52 (0.15), residues: 1206 sheet: 1.69 (0.35), residues: 198 loop : -0.59 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 308 TYR 0.008 0.001 TYR B 545 PHE 0.041 0.001 PHE E 246 TRP 0.006 0.001 TRP F 526 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00331 (19860) covalent geometry : angle 0.63353 (26850) hydrogen bonds : bond 0.06197 ( 678) hydrogen bonds : angle 4.88869 ( 1944) *********************** 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 118 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.746 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: 0.8486 (tpp) cc_final: 0.8098 (tpp) REVERT: A 308 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7905 (mtm-85) REVERT: A 333 MET cc_start: 0.8281 (tmm) cc_final: 0.8038 (tmm) REVERT: A 502 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 291 MET cc_start: 0.8055 (ttt) cc_final: 0.7451 (ptm) REVERT: B 308 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8359 (tpm170) REVERT: B 310 ASP cc_start: 0.8105 (m-30) cc_final: 0.7828 (m-30) REVERT: C 308 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.7799 (mmm-85) REVERT: C 310 ASP cc_start: 0.8844 (t0) cc_final: 0.8605 (t0) REVERT: C 520 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 391 MET cc_start: 0.8157 (tpp) cc_final: 0.7857 (tpp) REVERT: D 502 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8493 (tm-30) outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.1719 time to fit residues: 29.0268 Evaluate side-chains 103 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E 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 20 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 209 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 514 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.099082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.064370 restraints weight = 49391.796| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.26 r_work: 0.2683 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2219 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= 0.144 Angle : 0.582 11.311 26850 Z= 0.279 Chirality : 0.042 0.143 3102 Planarity : 0.004 0.039 3492 Dihedral : 8.646 137.929 2778 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.20 % Allowed : 7.53 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.17), residues: 2484 helix: -0.15 (0.15), residues: 1200 sheet: 1.90 (0.35), residues: 198 loop : -0.50 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 241 TYR 0.007 0.001 TYR B 545 PHE 0.042 0.001 PHE E 246 TRP 0.005 0.001 TRP F 526 HIS 0.003 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00323 (19860) covalent geometry : angle 0.58214 (26850) hydrogen bonds : bond 0.05383 ( 678) hydrogen bonds : angle 4.33105 ( 1944) *********************** 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 112 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8575 (tpp) cc_final: 0.8158 (tpp) REVERT: A 502 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 291 MET cc_start: 0.8254 (ttt) cc_final: 0.7755 (ptm) REVERT: B 308 ARG cc_start: 0.8735 (tpp-160) cc_final: 0.8280 (tpm170) REVERT: B 310 ASP cc_start: 0.8212 (m-30) cc_final: 0.7920 (m-30) REVERT: C 308 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.7965 (mmm-85) REVERT: C 310 ASP cc_start: 0.8767 (t0) cc_final: 0.8371 (t0) REVERT: C 520 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8048 (tm-30) REVERT: D 308 ARG cc_start: 0.9018 (mmm-85) cc_final: 0.8625 (tpp-160) REVERT: D 391 MET cc_start: 0.8189 (tpp) cc_final: 0.7806 (tpp) REVERT: D 502 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8598 (tm-30) REVERT: E 308 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.7755 (tpm170) REVERT: E 376 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8954 (mm-30) REVERT: F 260 ASP cc_start: 0.7988 (t0) cc_final: 0.7763 (p0) REVERT: F 318 ARG cc_start: 0.8762 (mmt180) cc_final: 0.8493 (mmt180) REVERT: F 376 GLU cc_start: 0.9363 (tp30) cc_final: 0.9058 (tp30) outliers start: 4 outliers final: 4 residues processed: 109 average time/residue: 0.1917 time to fit residues: 29.7048 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 : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 303 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 78 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 149 optimal weight: 0.3980 chunk 163 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 217 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.0470 chunk 34 optimal weight: 8.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 ASN C 343 HIS ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.064109 restraints weight = 48832.355| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.23 r_work: 0.2676 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.125 Angle : 0.549 9.609 26850 Z= 0.260 Chirality : 0.042 0.132 3102 Planarity : 0.004 0.036 3492 Dihedral : 7.656 121.552 2778 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.49 % Allowed : 9.38 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.18), residues: 2484 helix: 0.15 (0.15), residues: 1218 sheet: 2.08 (0.36), residues: 198 loop : -0.52 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 308 TYR 0.008 0.001 TYR B 545 PHE 0.032 0.001 PHE E 246 TRP 0.004 0.001 TRP E 526 HIS 0.004 0.001 HIS F 252 Details of bonding type rmsd covalent geometry : bond 0.00288 (19860) covalent geometry : angle 0.54897 (26850) hydrogen bonds : bond 0.04466 ( 678) hydrogen bonds : angle 3.90015 ( 1944) *********************** 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 109 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.720 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: 0.8682 (tpp) cc_final: 0.8264 (tpp) REVERT: A 502 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8401 (tm-30) REVERT: B 291 MET cc_start: 0.8322 (ttt) cc_final: 0.7795 (ptm) REVERT: B 308 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8260 (tpm170) REVERT: B 310 ASP cc_start: 0.8275 (m-30) cc_final: 0.7960 (m-30) REVERT: B 502 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 514 GLN cc_start: 0.8508 (mt0) cc_final: 0.8081 (mp10) REVERT: C 308 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: C 310 ASP cc_start: 0.8854 (t0) cc_final: 0.8456 (t0) REVERT: D 308 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8674 (mmm-85) REVERT: D 318 ARG cc_start: 0.8941 (tpt170) cc_final: 0.8716 (tpt170) REVERT: D 333 MET cc_start: 0.8117 (tmm) cc_final: 0.7913 (tmm) REVERT: D 502 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8579 (tm-30) REVERT: E 308 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8145 (mmm-85) REVERT: E 376 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9004 (mm-30) REVERT: F 260 ASP cc_start: 0.8295 (t0) cc_final: 0.7907 (p0) REVERT: F 318 ARG cc_start: 0.8838 (mmt180) cc_final: 0.8554 (mmm160) REVERT: F 376 GLU cc_start: 0.9360 (tp30) cc_final: 0.8998 (tp30) REVERT: F 514 GLN cc_start: 0.8417 (mt0) cc_final: 0.8063 (mp10) outliers start: 10 outliers final: 3 residues processed: 108 average time/residue: 0.1771 time to fit residues: 26.9613 Evaluate side-chains 98 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain E residue 242 VAL 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 137 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 D 187 ASN ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS E 252 HIS E 343 HIS F 285 ASN F 343 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.061070 restraints weight = 49104.978| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.16 r_work: 0.2655 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19860 Z= 0.189 Angle : 0.589 7.875 26850 Z= 0.283 Chirality : 0.043 0.149 3102 Planarity : 0.004 0.044 3492 Dihedral : 7.308 105.990 2778 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.78 % Allowed : 10.75 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 2484 helix: 0.34 (0.15), residues: 1212 sheet: 1.88 (0.35), residues: 198 loop : -0.56 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 243 TYR 0.009 0.001 TYR A 465 PHE 0.020 0.001 PHE E 246 TRP 0.004 0.001 TRP F 526 HIS 0.005 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00440 (19860) covalent geometry : angle 0.58886 (26850) hydrogen bonds : bond 0.05389 ( 678) hydrogen bonds : angle 4.05391 ( 1944) *********************** 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 109 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8132 (mtm-85) REVERT: A 502 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8619 (tm-30) REVERT: B 291 MET cc_start: 0.8277 (ttt) cc_final: 0.7713 (ptm) REVERT: B 308 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8337 (tpm170) REVERT: B 310 ASP cc_start: 0.8385 (m-30) cc_final: 0.8132 (m-30) REVERT: B 502 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8993 (tm-30) REVERT: B 514 GLN cc_start: 0.8625 (mt0) cc_final: 0.8211 (mp10) REVERT: C 308 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8164 (mmm-85) REVERT: C 310 ASP cc_start: 0.9054 (t0) cc_final: 0.8787 (t0) REVERT: D 308 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8690 (mmm-85) REVERT: D 318 ARG cc_start: 0.8946 (tpt170) cc_final: 0.8719 (tpt170) REVERT: E 308 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8227 (mmm-85) REVERT: E 318 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7612 (mmp80) REVERT: E 376 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8984 (mm-30) REVERT: F 260 ASP cc_start: 0.8390 (t0) cc_final: 0.7891 (p0) REVERT: F 318 ARG cc_start: 0.8836 (mmt180) cc_final: 0.8397 (mmm160) REVERT: F 376 GLU cc_start: 0.9384 (tp30) cc_final: 0.9017 (tp30) REVERT: F 514 GLN cc_start: 0.8521 (mt0) cc_final: 0.8212 (mp10) outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 0.1852 time to fit residues: 28.0234 Evaluate side-chains 98 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 467 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 108 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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 252 HIS F 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062540 restraints weight = 48760.802| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.21 r_work: 0.2687 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3319 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= 0.109 Angle : 0.537 9.694 26850 Z= 0.253 Chirality : 0.041 0.137 3102 Planarity : 0.003 0.035 3492 Dihedral : 6.992 100.710 2778 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.73 % Allowed : 11.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2484 helix: 0.62 (0.15), residues: 1230 sheet: 2.02 (0.35), residues: 198 loop : -0.50 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 308 TYR 0.008 0.001 TYR C 545 PHE 0.017 0.001 PHE E 186 TRP 0.004 0.001 TRP B 526 HIS 0.006 0.001 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00246 (19860) covalent geometry : angle 0.53707 (26850) hydrogen bonds : bond 0.04330 ( 678) hydrogen bonds : angle 3.67494 ( 1944) *********************** 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 111 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8600 (tm-30) REVERT: B 291 MET cc_start: 0.8277 (ttt) cc_final: 0.7711 (ptm) REVERT: B 308 ARG cc_start: 0.8716 (tpp-160) cc_final: 0.8366 (tpm170) REVERT: B 310 ASP cc_start: 0.8393 (m-30) cc_final: 0.8096 (m-30) REVERT: B 502 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8955 (tm-30) REVERT: B 514 GLN cc_start: 0.8567 (mt0) cc_final: 0.8174 (mp10) REVERT: C 308 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8146 (mmm-85) REVERT: C 310 ASP cc_start: 0.9046 (t0) cc_final: 0.8777 (t0) REVERT: D 308 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8697 (mmm-85) REVERT: D 310 ASP cc_start: 0.8939 (t0) cc_final: 0.8682 (t0) REVERT: D 318 ARG cc_start: 0.8927 (tpt170) cc_final: 0.8715 (tpt170) REVERT: E 308 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8373 (mmm-85) REVERT: E 318 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7790 (mmp80) REVERT: E 376 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8973 (mm-30) REVERT: F 260 ASP cc_start: 0.8355 (t0) cc_final: 0.7922 (p0) REVERT: F 318 ARG cc_start: 0.8793 (mmt180) cc_final: 0.8366 (mmm160) REVERT: F 376 GLU cc_start: 0.9364 (tp30) cc_final: 0.8966 (tp30) REVERT: F 514 GLN cc_start: 0.8497 (mt0) cc_final: 0.8184 (mp10) outliers start: 15 outliers final: 8 residues processed: 108 average time/residue: 0.1797 time to fit residues: 27.7649 Evaluate side-chains 100 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 467 VAL Chi-restraints excluded: chain E residue 242 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 0.0270 chunk 220 optimal weight: 0.2980 chunk 239 optimal weight: 0.7980 chunk 244 optimal weight: 0.0270 chunk 180 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 132 optimal weight: 0.0170 chunk 200 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.2134 ------------------------------------------------------------------------------- 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 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.064408 restraints weight = 48716.697| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.17 r_work: 0.2731 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19860 Z= 0.089 Angle : 0.524 9.607 26850 Z= 0.244 Chirality : 0.041 0.135 3102 Planarity : 0.003 0.033 3492 Dihedral : 6.698 94.574 2778 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.34 % Allowed : 11.93 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2484 helix: 1.04 (0.16), residues: 1206 sheet: 2.16 (0.35), residues: 198 loop : -0.43 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 241 TYR 0.008 0.001 TYR C 545 PHE 0.011 0.001 PHE E 230 TRP 0.005 0.001 TRP D 526 HIS 0.013 0.001 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00192 (19860) covalent geometry : angle 0.52356 (26850) hydrogen bonds : bond 0.03576 ( 678) hydrogen bonds : angle 3.35741 ( 1944) *********************** 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 104 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8620 (tpp) cc_final: 0.8321 (tpp) REVERT: A 308 ARG cc_start: 0.8351 (mtm110) cc_final: 0.8062 (mtm-85) REVERT: A 502 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 291 MET cc_start: 0.8343 (ttt) cc_final: 0.7798 (ptm) REVERT: B 308 ARG cc_start: 0.8811 (tpp-160) cc_final: 0.8472 (tpm170) REVERT: B 310 ASP cc_start: 0.8502 (m-30) cc_final: 0.8184 (m-30) REVERT: B 502 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8963 (tm-30) REVERT: B 514 GLN cc_start: 0.8570 (mt0) cc_final: 0.8195 (mp10) REVERT: C 308 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: C 310 ASP cc_start: 0.9095 (t0) cc_final: 0.8829 (t0) REVERT: D 310 ASP cc_start: 0.8864 (t0) cc_final: 0.8517 (t0) REVERT: D 318 ARG cc_start: 0.8917 (tpt170) cc_final: 0.8239 (mmm-85) REVERT: E 308 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8411 (mmm-85) REVERT: E 318 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.7763 (mmp80) REVERT: F 260 ASP cc_start: 0.8346 (t0) cc_final: 0.7900 (p0) REVERT: F 318 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8194 (mmm160) REVERT: F 376 GLU cc_start: 0.9356 (tp30) cc_final: 0.8926 (tp30) REVERT: F 514 GLN cc_start: 0.8504 (mt0) cc_final: 0.8208 (mp10) outliers start: 7 outliers final: 6 residues processed: 103 average time/residue: 0.2097 time to fit residues: 30.6119 Evaluate side-chains 97 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 242 VAL Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 316 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 40 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 0.0980 chunk 241 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.062063 restraints weight = 48055.886| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.25 r_work: 0.2697 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19860 Z= 0.126 Angle : 0.533 8.718 26850 Z= 0.248 Chirality : 0.042 0.133 3102 Planarity : 0.003 0.037 3492 Dihedral : 6.530 91.566 2778 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.39 % Allowed : 12.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2484 helix: 1.20 (0.16), residues: 1206 sheet: 2.09 (0.35), residues: 198 loop : -0.44 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 243 TYR 0.007 0.001 TYR F 545 PHE 0.008 0.001 PHE E 246 TRP 0.004 0.001 TRP C 526 HIS 0.009 0.001 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00295 (19860) covalent geometry : angle 0.53306 (26850) hydrogen bonds : bond 0.04065 ( 678) hydrogen bonds : angle 3.46579 ( 1944) *********************** 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 104 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8656 (tpp) cc_final: 0.8342 (tpp) REVERT: A 308 ARG cc_start: 0.8341 (mtm110) cc_final: 0.8011 (mtm-85) REVERT: A 502 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8702 (tm-30) REVERT: B 291 MET cc_start: 0.8352 (ttt) cc_final: 0.7771 (ptm) REVERT: B 308 ARG cc_start: 0.8801 (tpp-160) cc_final: 0.8462 (tpm170) REVERT: B 310 ASP cc_start: 0.8536 (m-30) cc_final: 0.8265 (m-30) REVERT: B 502 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8994 (tm-30) REVERT: B 514 GLN cc_start: 0.8633 (mt0) cc_final: 0.8245 (mp10) REVERT: C 308 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: C 310 ASP cc_start: 0.9116 (t0) cc_final: 0.8870 (t0) REVERT: D 308 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8405 (tpp-160) REVERT: D 318 ARG cc_start: 0.8924 (tpt170) cc_final: 0.8260 (mmm-85) REVERT: E 308 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8622 (mmm-85) REVERT: F 260 ASP cc_start: 0.8369 (t0) cc_final: 0.7922 (p0) REVERT: F 318 ARG cc_start: 0.8781 (mmt180) cc_final: 0.8504 (mmm160) REVERT: F 376 GLU cc_start: 0.9381 (tp30) cc_final: 0.8964 (tp30) REVERT: F 514 GLN cc_start: 0.8586 (mt0) cc_final: 0.8309 (mp10) outliers start: 8 outliers final: 7 residues processed: 104 average time/residue: 0.1855 time to fit residues: 27.6147 Evaluate side-chains 103 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 467 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 153 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 204 optimal weight: 0.0370 chunk 49 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.2262 ------------------------------------------------------------------------------- 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 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.061833 restraints weight = 48017.113| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.24 r_work: 0.2684 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19860 Z= 0.141 Angle : 0.550 11.532 26850 Z= 0.257 Chirality : 0.042 0.140 3102 Planarity : 0.003 0.035 3492 Dihedral : 6.328 83.782 2778 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.34 % Allowed : 12.46 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2484 helix: 1.27 (0.16), residues: 1206 sheet: 2.02 (0.35), residues: 198 loop : -0.44 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 243 TYR 0.008 0.001 TYR F 545 PHE 0.008 0.001 PHE E 246 TRP 0.004 0.001 TRP C 526 HIS 0.011 0.001 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00330 (19860) covalent geometry : angle 0.54966 (26850) hydrogen bonds : bond 0.04267 ( 678) hydrogen bonds : angle 3.53507 ( 1944) *********************** 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 101 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8719 (tpp) cc_final: 0.8395 (tpp) REVERT: A 308 ARG cc_start: 0.8313 (mtm110) cc_final: 0.8074 (mtm-85) REVERT: A 502 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 291 MET cc_start: 0.8366 (ttt) cc_final: 0.7780 (ptm) REVERT: B 308 ARG cc_start: 0.8793 (tpp-160) cc_final: 0.8405 (tpm170) REVERT: B 310 ASP cc_start: 0.8639 (m-30) cc_final: 0.8384 (m-30) REVERT: B 502 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9024 (tm-30) REVERT: B 514 GLN cc_start: 0.8693 (mt0) cc_final: 0.8296 (mp10) REVERT: C 308 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: D 308 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8444 (tpp-160) REVERT: D 318 ARG cc_start: 0.8941 (tpt170) cc_final: 0.8295 (mmm-85) REVERT: E 376 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8989 (mm-30) REVERT: F 260 ASP cc_start: 0.8516 (t0) cc_final: 0.8111 (p0) REVERT: F 318 ARG cc_start: 0.8787 (mmt180) cc_final: 0.8514 (mmm160) REVERT: F 376 GLU cc_start: 0.9368 (tp30) cc_final: 0.8934 (tp30) REVERT: F 514 GLN cc_start: 0.8606 (mt0) cc_final: 0.8355 (mp10) outliers start: 7 outliers final: 7 residues processed: 101 average time/residue: 0.1841 time to fit residues: 26.9977 Evaluate side-chains 99 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 467 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 202 optimal weight: 0.2980 chunk 225 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 213 optimal weight: 0.0470 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.063275 restraints weight = 48652.570| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.20 r_work: 0.2666 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3726 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= 0.098 Angle : 0.537 11.089 26850 Z= 0.249 Chirality : 0.041 0.140 3102 Planarity : 0.003 0.037 3492 Dihedral : 6.139 89.240 2778 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.24 % Allowed : 12.76 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.18), residues: 2484 helix: 1.44 (0.16), residues: 1206 sheet: 2.11 (0.35), residues: 198 loop : -0.43 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 243 TYR 0.007 0.001 TYR F 545 PHE 0.008 0.001 PHE E 230 TRP 0.005 0.001 TRP D 526 HIS 0.010 0.001 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00225 (19860) covalent geometry : angle 0.53732 (26850) hydrogen bonds : bond 0.03844 ( 678) hydrogen bonds : angle 3.34813 ( 1944) ********************** 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 102 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.773 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: 0.8700 (tpp) cc_final: 0.8375 (tpp) REVERT: A 308 ARG cc_start: 0.8294 (mtm110) cc_final: 0.8003 (mtm-85) REVERT: A 502 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 291 MET cc_start: 0.8362 (ttt) cc_final: 0.7785 (ptm) REVERT: B 308 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8379 (tpm170) REVERT: B 310 ASP cc_start: 0.8644 (m-30) cc_final: 0.8386 (m-30) REVERT: B 502 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9010 (tm-30) REVERT: B 514 GLN cc_start: 0.8609 (mt0) cc_final: 0.8216 (mp10) REVERT: D 308 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8453 (tpp-160) REVERT: D 318 ARG cc_start: 0.8929 (tpt170) cc_final: 0.8299 (mmm-85) REVERT: E 308 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.7849 (tpm170) REVERT: E 376 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9137 (mm-30) REVERT: F 260 ASP cc_start: 0.8522 (t0) cc_final: 0.8120 (p0) REVERT: F 318 ARG cc_start: 0.8631 (mmt180) cc_final: 0.8366 (mmm160) REVERT: F 376 GLU cc_start: 0.9353 (tp30) cc_final: 0.8881 (tp30) REVERT: F 514 GLN cc_start: 0.8560 (mt0) cc_final: 0.8310 (mp10) outliers start: 5 outliers final: 5 residues processed: 102 average time/residue: 0.1967 time to fit residues: 28.6859 Evaluate side-chains 97 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 467 VAL Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4767 > 50: distance: 48 - 142: 31.998 distance: 95 - 98: 19.977 distance: 98 - 99: 21.877 distance: 99 - 100: 48.628 distance: 99 - 102: 35.344 distance: 100 - 101: 17.157 distance: 100 - 103: 18.264 distance: 103 - 104: 26.625 distance: 104 - 105: 20.530 distance: 104 - 107: 16.314 distance: 105 - 106: 29.214 distance: 105 - 108: 16.036 distance: 108 - 109: 19.875 distance: 109 - 110: 23.894 distance: 109 - 112: 11.782 distance: 110 - 111: 12.538 distance: 110 - 116: 26.504 distance: 112 - 113: 22.766 distance: 113 - 114: 33.178 distance: 113 - 115: 35.048 distance: 116 - 117: 40.578 distance: 117 - 118: 33.113 distance: 118 - 119: 54.772 distance: 118 - 120: 34.981 distance: 120 - 121: 11.336 distance: 121 - 122: 16.527 distance: 121 - 124: 23.754 distance: 122 - 123: 16.440 distance: 122 - 132: 10.166 distance: 124 - 125: 24.584 distance: 125 - 126: 18.332 distance: 125 - 127: 16.233 distance: 126 - 128: 8.966 distance: 127 - 129: 20.236 distance: 128 - 130: 7.055 distance: 129 - 130: 5.643 distance: 130 - 131: 24.346 distance: 132 - 133: 11.149 distance: 133 - 134: 27.754 distance: 133 - 136: 15.270 distance: 134 - 135: 30.180 distance: 134 - 139: 16.902 distance: 136 - 137: 17.440 distance: 136 - 138: 31.209 distance: 139 - 140: 21.613 distance: 140 - 141: 21.172 distance: 140 - 143: 16.346 distance: 141 - 142: 18.872 distance: 141 - 147: 14.935 distance: 143 - 144: 23.299 distance: 144 - 145: 8.296 distance: 144 - 146: 38.122 distance: 147 - 148: 20.493 distance: 148 - 149: 35.401 distance: 148 - 151: 33.658 distance: 149 - 150: 6.961 distance: 149 - 157: 17.589 distance: 151 - 152: 31.215 distance: 152 - 153: 27.743 distance: 152 - 154: 20.214 distance: 153 - 155: 31.566 distance: 154 - 156: 10.905 distance: 155 - 156: 7.776 distance: 157 - 158: 3.548 distance: 158 - 159: 27.317 distance: 158 - 161: 16.547 distance: 159 - 160: 6.831 distance: 159 - 165: 31.067 distance: 161 - 162: 43.157 distance: 162 - 163: 38.236 distance: 162 - 164: 29.423 distance: 165 - 166: 26.702 distance: 165 - 171: 22.286 distance: 167 - 172: 35.196 distance: 169 - 170: 13.218 distance: 170 - 171: 15.829