Starting phenix.real_space_refine on Fri May 16 18:24:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tk0_41319/05_2025/8tk0_41319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tk0_41319/05_2025/8tk0_41319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tk0_41319/05_2025/8tk0_41319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tk0_41319/05_2025/8tk0_41319.map" model { file = "/net/cci-nas-00/data/ceres_data/8tk0_41319/05_2025/8tk0_41319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tk0_41319/05_2025/8tk0_41319.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9516 2.51 5 N 2440 2.21 5 O 2812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3704 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3704 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3704 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3704 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.21, per 1000 atoms: 0.76 Number of scatterers: 14816 At special positions: 0 Unit cell: (70.122, 195.532, 114.173, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2812 8.00 N 2440 7.00 C 9516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 18 sheets defined 40.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.514A pdb=" N LYS A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.699A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.513A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.772A pdb=" N GLY A 356 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 357' Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.436A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.860A pdb=" N ILE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.591A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 475 through 493 removed outlier: 3.520A pdb=" N LYS A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.648A pdb=" N GLY A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.718A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.643A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.577A pdb=" N GLU A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 563 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.449A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.792A pdb=" N LYS B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.700A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.562A pdb=" N GLN B 299 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.494A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 removed outlier: 4.022A pdb=" N LYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 3.586A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.540A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.627A pdb=" N GLN B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.817A pdb=" N GLY B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 525 removed outlier: 3.512A pdb=" N SER B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.567A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.694A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 563 removed outlier: 3.550A pdb=" N GLU B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 563 " --> pdb=" O ASP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 567 Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.607A pdb=" N LEU B 572 " --> pdb=" O CYS B 568 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 568 through 574' Processing helix chain 'C' and resid 31 through 41 removed outlier: 3.644A pdb=" N LYS C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.753A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.524A pdb=" N ARG C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.555A pdb=" N GLN C 299 " --> pdb=" O HIS C 295 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.704A pdb=" N TYR C 355 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 356' Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.337A pdb=" N LYS C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.695A pdb=" N LYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.563A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 475 through 493 removed outlier: 3.665A pdb=" N TYR C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.662A pdb=" N GLY C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 525 removed outlier: 3.566A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.619A pdb=" N GLN C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.627A pdb=" N GLU C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 559 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 568 through 574 removed outlier: 3.631A pdb=" N LEU C 572 " --> pdb=" O CYS C 568 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY C 574 " --> pdb=" O LYS C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 574' Processing helix chain 'D' and resid 33 through 47 removed outlier: 3.899A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 removed outlier: 4.241A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 removed outlier: 3.502A pdb=" N ASN D 147 " --> pdb=" O ALA D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 147' Processing helix chain 'D' and resid 295 through 309 removed outlier: 3.621A pdb=" N GLN D 299 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 4.478A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 removed outlier: 4.052A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 3.559A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 423 " --> pdb=" O THR D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.959A pdb=" N LEU D 456 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 493 removed outlier: 3.645A pdb=" N TYR D 493 " --> pdb=" O ILE D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.720A pdb=" N GLY D 502 " --> pdb=" O GLY D 498 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 525 removed outlier: 3.649A pdb=" N ASP D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 525 " --> pdb=" O GLY D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.588A pdb=" N GLN D 538 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 551 removed outlier: 3.803A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 563 removed outlier: 3.529A pdb=" N CYS D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 562 " --> pdb=" O PHE D 558 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 563 " --> pdb=" O ASP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 567 through 574 removed outlier: 3.848A pdb=" N GLU D 571 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 572 " --> pdb=" O CYS D 568 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY D 574 " --> pdb=" O LYS D 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 7.203A pdb=" N GLU A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 2 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE A 6 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 72 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A 8 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLU A 70 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 119 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.692A pdb=" N LYS A 24 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 334 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 407 removed outlier: 7.768A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 430 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.537A pdb=" N LYS A 436 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 20 removed outlier: 7.243A pdb=" N GLU B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 2 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 74 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 6 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 72 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 8 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU B 70 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 127 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 3.531A pdb=" N SER B 318 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 24 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE B 334 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 405 through 407 removed outlier: 7.807A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 430 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.576A pdb=" N LYS B 436 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 14 through 20 removed outlier: 7.239A pdb=" N GLU C 15 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 2 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.541A pdb=" N SER C 318 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 114 Processing sheet with id=AB3, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.930A pdb=" N LYS C 430 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 436 through 437 Processing sheet with id=AB5, first strand: chain 'D' and resid 14 through 20 removed outlier: 7.257A pdb=" N GLU D 15 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 2 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR D 74 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE D 6 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE D 72 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE D 8 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU D 70 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 69 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 127 " --> pdb=" O TYR D 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 149 through 154 removed outlier: 3.553A pdb=" N SER D 318 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS D 24 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE D 334 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 113 through 114 removed outlier: 3.516A pdb=" N TYR D 119 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 405 through 407 removed outlier: 7.816A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 430 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 435 through 437 523 hydrogen bonds defined for protein. 1497 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: 4.20 Time building geometry restraints manager: 3.72 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: 4775 1.34 - 1.46: 2324 1.46 - 1.57: 7893 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 15068 Sorted by residual: bond pdb=" CA ASP B 532 " pdb=" CB ASP B 532 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.58e-02 4.01e+03 8.83e-01 bond pdb=" CB TRP B 126 " pdb=" CG TRP B 126 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 7.98e-01 bond pdb=" C VAL A 358 " pdb=" O VAL A 358 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.94e-01 bond pdb=" N ASP B 532 " pdb=" CA ASP B 532 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.41e-02 5.03e+03 7.44e-01 bond pdb=" C VAL D 358 " pdb=" O VAL D 358 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.89e-01 ... (remaining 15063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 19401 1.32 - 2.65: 685 2.65 - 3.97: 113 3.97 - 5.30: 25 5.30 - 6.62: 20 Bond angle restraints: 20244 Sorted by residual: angle pdb=" N ILE B 90 " pdb=" CA ILE B 90 " pdb=" C ILE B 90 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.08e+01 angle pdb=" N VAL C 358 " pdb=" CA VAL C 358 " pdb=" C VAL C 358 " ideal model delta sigma weight residual 111.88 108.04 3.84 1.06e+00 8.90e-01 1.31e+01 angle pdb=" N ILE B 136 " pdb=" CA ILE B 136 " pdb=" C ILE B 136 " ideal model delta sigma weight residual 108.63 111.32 -2.69 8.60e-01 1.35e+00 9.78e+00 angle pdb=" N TYR A 493 " pdb=" CA TYR A 493 " pdb=" C TYR A 493 " ideal model delta sigma weight residual 110.44 114.18 -3.74 1.20e+00 6.94e-01 9.69e+00 angle pdb=" N TRP B 126 " pdb=" CA TRP B 126 " pdb=" CB TRP B 126 " ideal model delta sigma weight residual 110.14 115.45 -5.31 1.72e+00 3.38e-01 9.52e+00 ... (remaining 20239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 8147 17.49 - 34.98: 866 34.98 - 52.47: 153 52.47 - 69.96: 21 69.96 - 87.44: 9 Dihedral angle restraints: 9196 sinusoidal: 3864 harmonic: 5332 Sorted by residual: dihedral pdb=" CA GLN C 492 " pdb=" C GLN C 492 " pdb=" N TYR C 493 " pdb=" CA TYR C 493 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG A 12 " pdb=" CD ARG A 12 " pdb=" NE ARG A 12 " pdb=" CZ ARG A 12 " ideal model delta sinusoidal sigma weight residual 90.00 133.93 -43.93 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU D 562 " pdb=" CG GLU D 562 " pdb=" CD GLU D 562 " pdb=" OE1 GLU D 562 " ideal model delta sinusoidal sigma weight residual 0.00 87.44 -87.44 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1233 0.031 - 0.062: 656 0.062 - 0.093: 226 0.093 - 0.123: 124 0.123 - 0.154: 21 Chirality restraints: 2260 Sorted by residual: chirality pdb=" CB ILE B 136 " pdb=" CA ILE B 136 " pdb=" CG1 ILE B 136 " pdb=" CG2 ILE B 136 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE A 428 " pdb=" N ILE A 428 " pdb=" C ILE A 428 " pdb=" CB ILE A 428 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE D 428 " pdb=" N ILE D 428 " pdb=" C ILE D 428 " pdb=" CB ILE D 428 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2257 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 126 " 0.046 2.00e-02 2.50e+03 3.80e-02 3.60e+01 pdb=" CG TRP B 126 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP B 126 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 126 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 126 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 126 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 126 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 126 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 126 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 126 " -0.041 2.00e-02 2.50e+03 3.38e-02 2.86e+01 pdb=" CG TRP A 126 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP A 126 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 126 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 126 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 126 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 126 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 126 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 126 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 126 " 0.035 2.00e-02 2.50e+03 3.08e-02 2.38e+01 pdb=" CG TRP D 126 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP D 126 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP D 126 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 126 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 126 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 126 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 126 " 0.003 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2189 2.76 - 3.30: 13047 3.30 - 3.83: 20871 3.83 - 4.37: 24339 4.37 - 4.90: 44106 Nonbonded interactions: 104552 Sorted by model distance: nonbonded pdb=" OH TYR C 153 " pdb=" OE1 GLU C 288 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 540 " pdb=" OD1 ASN A 544 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 153 " pdb=" OE1 GLU A 288 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 303 " pdb=" O LEU B 324 " model vdw 2.264 3.040 ... (remaining 104547 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 24.990 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.870 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 0.028 15068 Z= 0.179 Angle : 0.614 6.621 20244 Z= 0.341 Chirality : 0.046 0.154 2260 Planarity : 0.003 0.038 2572 Dihedral : 14.443 87.444 5756 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1800 helix: 0.41 (0.22), residues: 572 sheet: 0.61 (0.27), residues: 420 loop : -2.34 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.019 TRP B 126 HIS 0.005 0.001 HIS B 63 PHE 0.022 0.002 PHE C 53 TYR 0.030 0.002 TYR A 326 ARG 0.006 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.21466 ( 523) hydrogen bonds : angle 7.26775 ( 1497) covalent geometry : bond 0.00407 (15068) covalent geometry : angle 0.61424 (20244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7750 (m-30) cc_final: 0.7540 (m-30) REVERT: A 289 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 367 SER cc_start: 0.8504 (p) cc_final: 0.8256 (p) REVERT: B 10 ASN cc_start: 0.8518 (m110) cc_final: 0.8237 (m110) REVERT: B 84 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7050 (mm-30) REVERT: B 341 LYS cc_start: 0.7865 (tptp) cc_final: 0.7096 (tptp) REVERT: B 397 GLU cc_start: 0.7475 (pt0) cc_final: 0.7212 (pt0) REVERT: B 494 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7545 (mmmm) REVERT: B 513 GLU cc_start: 0.6685 (mp0) cc_final: 0.6294 (mp0) REVERT: B 551 ASN cc_start: 0.8503 (m110) cc_final: 0.8267 (m110) REVERT: C 434 ASP cc_start: 0.7650 (t0) cc_final: 0.7433 (t0) REVERT: D 84 GLU cc_start: 0.7802 (tp30) cc_final: 0.7391 (tp30) REVERT: D 289 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7907 (mm-30) REVERT: D 341 LYS cc_start: 0.7772 (tptt) cc_final: 0.7496 (tptt) REVERT: D 367 SER cc_start: 0.8520 (p) cc_final: 0.8292 (p) REVERT: D 464 GLU cc_start: 0.7869 (mp0) cc_final: 0.7620 (mp0) REVERT: D 488 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7790 (mm-30) REVERT: D 511 ASP cc_start: 0.7566 (t0) cc_final: 0.7225 (t0) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.2672 time to fit residues: 192.0655 Evaluate side-chains 469 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 25 ASN B 143 ASN B 295 HIS C 143 ASN D 10 ASN D 25 ASN D 295 HIS D 415 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109897 restraints weight = 20547.555| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.57 r_work: 0.3229 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15068 Z= 0.162 Angle : 0.578 7.774 20244 Z= 0.308 Chirality : 0.044 0.140 2260 Planarity : 0.003 0.027 2572 Dihedral : 4.239 18.595 1952 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.32 % Allowed : 9.25 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1800 helix: 0.56 (0.23), residues: 576 sheet: 0.49 (0.25), residues: 460 loop : -2.18 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.011 TRP A 126 HIS 0.005 0.001 HIS B 63 PHE 0.017 0.002 PHE A 315 TYR 0.019 0.002 TYR A 326 ARG 0.005 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05572 ( 523) hydrogen bonds : angle 5.46233 ( 1497) covalent geometry : bond 0.00375 (15068) covalent geometry : angle 0.57765 (20244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 457 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.8052 (mp) cc_final: 0.7790 (mt) REVERT: A 131 ASP cc_start: 0.8161 (m-30) cc_final: 0.7940 (m-30) REVERT: A 289 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 306 LEU cc_start: 0.8356 (mt) cc_final: 0.8080 (mp) REVERT: A 367 SER cc_start: 0.8510 (p) cc_final: 0.8252 (p) REVERT: B 84 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 306 LEU cc_start: 0.8483 (mt) cc_final: 0.8197 (mp) REVERT: B 341 LYS cc_start: 0.7804 (tptp) cc_final: 0.7095 (tptp) REVERT: B 397 GLU cc_start: 0.8103 (pt0) cc_final: 0.7858 (pt0) REVERT: B 551 ASN cc_start: 0.7947 (m110) cc_final: 0.7585 (m-40) REVERT: C 84 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7333 (mm-30) REVERT: C 524 MET cc_start: 0.8243 (tpp) cc_final: 0.7930 (mmm) REVERT: D 30 MET cc_start: 0.8474 (ttp) cc_final: 0.8267 (ttm) REVERT: D 84 GLU cc_start: 0.7978 (tp30) cc_final: 0.7573 (tp30) REVERT: D 135 ASP cc_start: 0.7604 (t0) cc_final: 0.7328 (t0) REVERT: D 294 LEU cc_start: 0.8815 (mt) cc_final: 0.8612 (mt) REVERT: D 341 LYS cc_start: 0.7720 (tptt) cc_final: 0.7384 (tptt) REVERT: D 367 SER cc_start: 0.8478 (p) cc_final: 0.8242 (p) REVERT: D 464 GLU cc_start: 0.8049 (mp0) cc_final: 0.7815 (mp0) REVERT: D 484 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8145 (mm-30) outliers start: 22 outliers final: 17 residues processed: 464 average time/residue: 0.2706 time to fit residues: 179.4689 Evaluate side-chains 451 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 434 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 113 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 13 ASN A 143 ASN A 455 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 337 HIS B 427 HIS C 10 ASN C 143 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108619 restraints weight = 20577.143| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.55 r_work: 0.3223 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15068 Z= 0.181 Angle : 0.572 6.680 20244 Z= 0.306 Chirality : 0.044 0.137 2260 Planarity : 0.003 0.035 2572 Dihedral : 4.273 18.793 1952 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 2.40 % Allowed : 12.44 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 1800 helix: 0.56 (0.23), residues: 568 sheet: 0.61 (0.26), residues: 452 loop : -2.15 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.008 TRP D 126 HIS 0.006 0.001 HIS B 63 PHE 0.018 0.002 PHE A 315 TYR 0.016 0.002 TYR D 326 ARG 0.006 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05655 ( 523) hydrogen bonds : angle 5.33385 ( 1497) covalent geometry : bond 0.00425 (15068) covalent geometry : angle 0.57239 (20244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 443 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8138 (m-30) cc_final: 0.7914 (m-30) REVERT: A 289 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 306 LEU cc_start: 0.8375 (mt) cc_final: 0.8084 (mp) REVERT: A 565 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8708 (mttt) REVERT: B 84 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 306 LEU cc_start: 0.8534 (mt) cc_final: 0.8218 (mp) REVERT: B 341 LYS cc_start: 0.7805 (tptp) cc_final: 0.7111 (tptp) REVERT: B 355 TYR cc_start: 0.8019 (m-10) cc_final: 0.7668 (m-10) REVERT: B 397 GLU cc_start: 0.8071 (pt0) cc_final: 0.7831 (pt0) REVERT: B 551 ASN cc_start: 0.7979 (m110) cc_final: 0.7612 (m-40) REVERT: C 59 ASP cc_start: 0.8168 (m-30) cc_final: 0.7857 (m-30) REVERT: C 84 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 510 ILE cc_start: 0.8786 (mp) cc_final: 0.8332 (mt) REVERT: D 84 GLU cc_start: 0.7981 (tp30) cc_final: 0.7570 (tp30) REVERT: D 135 ASP cc_start: 0.7594 (t0) cc_final: 0.7351 (t0) REVERT: D 464 GLU cc_start: 0.8047 (mp0) cc_final: 0.7832 (mp0) REVERT: D 484 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8119 (mm-30) outliers start: 40 outliers final: 26 residues processed: 460 average time/residue: 0.2816 time to fit residues: 184.5505 Evaluate side-chains 454 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 428 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 401 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 141 optimal weight: 0.0470 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 0.0060 chunk 154 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 10 ASN A 143 ASN B 5 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 10 ASN C 143 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 143 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111913 restraints weight = 20473.883| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.55 r_work: 0.3275 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15068 Z= 0.095 Angle : 0.497 6.263 20244 Z= 0.265 Chirality : 0.042 0.136 2260 Planarity : 0.002 0.025 2572 Dihedral : 3.990 17.945 1952 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.16 % Allowed : 14.18 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1800 helix: 0.76 (0.23), residues: 584 sheet: 0.78 (0.26), residues: 452 loop : -2.07 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 126 HIS 0.003 0.000 HIS B 63 PHE 0.013 0.001 PHE A 14 TYR 0.016 0.001 TYR B 113 ARG 0.003 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 523) hydrogen bonds : angle 4.92275 ( 1497) covalent geometry : bond 0.00205 (15068) covalent geometry : angle 0.49688 (20244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 426 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8584 (m-80) cc_final: 0.8365 (m-80) REVERT: A 131 ASP cc_start: 0.8138 (m-30) cc_final: 0.7916 (m-30) REVERT: A 463 ASP cc_start: 0.7501 (m-30) cc_final: 0.7284 (m-30) REVERT: A 464 GLU cc_start: 0.7799 (mp0) cc_final: 0.7343 (mt-10) REVERT: A 565 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8712 (mttt) REVERT: B 84 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 113 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6884 (t80) REVERT: B 306 LEU cc_start: 0.8448 (mt) cc_final: 0.8126 (mp) REVERT: B 341 LYS cc_start: 0.7770 (tptp) cc_final: 0.7039 (tptp) REVERT: B 355 TYR cc_start: 0.7967 (m-10) cc_final: 0.7579 (m-10) REVERT: B 397 GLU cc_start: 0.8068 (pt0) cc_final: 0.7828 (pt0) REVERT: B 526 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7821 (ttp80) REVERT: B 551 ASN cc_start: 0.7686 (m110) cc_final: 0.7438 (m-40) REVERT: C 84 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7282 (mm-30) REVERT: C 524 MET cc_start: 0.8207 (tpp) cc_final: 0.7881 (mmm) REVERT: D 84 GLU cc_start: 0.7943 (tp30) cc_final: 0.7543 (tp30) REVERT: D 135 ASP cc_start: 0.7490 (t0) cc_final: 0.7279 (t0) REVERT: D 341 LYS cc_start: 0.7656 (tptt) cc_final: 0.7198 (tptt) REVERT: D 423 LEU cc_start: 0.8335 (mt) cc_final: 0.8094 (mp) REVERT: D 464 GLU cc_start: 0.8012 (mp0) cc_final: 0.7789 (mp0) REVERT: D 484 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8060 (mm-30) REVERT: D 510 ILE cc_start: 0.8795 (mp) cc_final: 0.8465 (mp) REVERT: D 544 ASN cc_start: 0.8775 (m110) cc_final: 0.8544 (m110) outliers start: 36 outliers final: 22 residues processed: 440 average time/residue: 0.2790 time to fit residues: 174.8926 Evaluate side-chains 438 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 415 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 4.9990 chunk 151 optimal weight: 0.1980 chunk 173 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 75 optimal weight: 0.0270 chunk 115 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 13 ASN A 143 ASN A 455 ASN B 5 ASN B 25 ASN B 143 ASN D 25 ASN D 141 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108368 restraints weight = 20737.773| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.55 r_work: 0.3216 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 15068 Z= 0.201 Angle : 0.576 7.780 20244 Z= 0.306 Chirality : 0.044 0.135 2260 Planarity : 0.003 0.042 2572 Dihedral : 4.229 19.510 1952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 3.12 % Allowed : 14.36 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1800 helix: 0.65 (0.23), residues: 576 sheet: 0.81 (0.26), residues: 444 loop : -2.20 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 126 HIS 0.005 0.001 HIS B 63 PHE 0.019 0.002 PHE D 315 TYR 0.017 0.002 TYR B 113 ARG 0.005 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05633 ( 523) hydrogen bonds : angle 5.22726 ( 1497) covalent geometry : bond 0.00477 (15068) covalent geometry : angle 0.57577 (20244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 434 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8154 (m-30) cc_final: 0.7931 (m-30) REVERT: A 341 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7178 (mmmt) REVERT: A 565 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8747 (mttt) REVERT: B 64 ASP cc_start: 0.8136 (t0) cc_final: 0.7919 (t0) REVERT: B 84 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 306 LEU cc_start: 0.8532 (mt) cc_final: 0.8205 (mp) REVERT: B 341 LYS cc_start: 0.7795 (tptp) cc_final: 0.7098 (tptp) REVERT: B 397 GLU cc_start: 0.8091 (pt0) cc_final: 0.7854 (pt0) REVERT: B 551 ASN cc_start: 0.7990 (m110) cc_final: 0.7645 (m-40) REVERT: C 84 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7312 (mm-30) REVERT: D 84 GLU cc_start: 0.7991 (tp30) cc_final: 0.7603 (tp30) REVERT: D 341 LYS cc_start: 0.7700 (tptt) cc_final: 0.7289 (tptt) REVERT: D 484 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8100 (mm-30) REVERT: D 544 ASN cc_start: 0.8820 (m110) cc_final: 0.8592 (m110) outliers start: 52 outliers final: 36 residues processed: 459 average time/residue: 0.2842 time to fit residues: 186.1795 Evaluate side-chains 466 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 429 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 401 ASN Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 10 ASN A 13 ASN A 143 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 10 ASN C 143 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109673 restraints weight = 20654.141| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.57 r_work: 0.3237 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15068 Z= 0.139 Angle : 0.538 6.993 20244 Z= 0.285 Chirality : 0.043 0.136 2260 Planarity : 0.003 0.027 2572 Dihedral : 4.131 18.575 1952 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.94 % Allowed : 16.17 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1800 helix: 0.69 (0.23), residues: 576 sheet: 0.86 (0.26), residues: 444 loop : -2.10 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 126 HIS 0.004 0.001 HIS B 63 PHE 0.015 0.001 PHE A 315 TYR 0.015 0.001 TYR B 113 ARG 0.004 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 523) hydrogen bonds : angle 5.06890 ( 1497) covalent geometry : bond 0.00323 (15068) covalent geometry : angle 0.53755 (20244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 423 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8145 (m-30) cc_final: 0.7921 (m-30) REVERT: A 463 ASP cc_start: 0.7532 (m-30) cc_final: 0.7297 (m-30) REVERT: A 464 GLU cc_start: 0.7825 (mp0) cc_final: 0.7327 (mt-10) REVERT: B 64 ASP cc_start: 0.8118 (t0) cc_final: 0.7893 (t0) REVERT: B 84 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 306 LEU cc_start: 0.8519 (mt) cc_final: 0.8189 (mp) REVERT: B 341 LYS cc_start: 0.7798 (tptp) cc_final: 0.7083 (tptp) REVERT: B 464 GLU cc_start: 0.8128 (mp0) cc_final: 0.7452 (mt-10) REVERT: B 526 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7862 (ttp80) REVERT: B 551 ASN cc_start: 0.7893 (m110) cc_final: 0.7600 (m-40) REVERT: C 84 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7297 (mm-30) REVERT: D 84 GLU cc_start: 0.7989 (tp30) cc_final: 0.7597 (tp30) REVERT: D 135 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: D 341 LYS cc_start: 0.7698 (tptt) cc_final: 0.7278 (tptt) REVERT: D 399 GLU cc_start: 0.8370 (tt0) cc_final: 0.8143 (tt0) REVERT: D 484 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8082 (mm-30) REVERT: D 544 ASN cc_start: 0.8793 (m110) cc_final: 0.8555 (m110) outliers start: 49 outliers final: 39 residues processed: 443 average time/residue: 0.2844 time to fit residues: 179.7335 Evaluate side-chains 452 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 412 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 0.0000 chunk 20 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 153 optimal weight: 0.0030 chunk 32 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 143 ASN B 5 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 10 ASN C 143 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110219 restraints weight = 20564.426| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.55 r_work: 0.3247 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15068 Z= 0.126 Angle : 0.528 6.426 20244 Z= 0.279 Chirality : 0.043 0.138 2260 Planarity : 0.002 0.024 2572 Dihedral : 4.051 17.980 1952 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.82 % Allowed : 16.65 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1800 helix: 0.78 (0.23), residues: 584 sheet: 0.90 (0.26), residues: 444 loop : -2.15 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 126 HIS 0.004 0.001 HIS B 63 PHE 0.014 0.001 PHE B 38 TYR 0.015 0.001 TYR B 113 ARG 0.004 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 523) hydrogen bonds : angle 4.99007 ( 1497) covalent geometry : bond 0.00289 (15068) covalent geometry : angle 0.52753 (20244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 432 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8139 (m-30) cc_final: 0.7918 (m-30) REVERT: A 463 ASP cc_start: 0.7516 (m-30) cc_final: 0.7299 (m-30) REVERT: A 464 GLU cc_start: 0.7821 (mp0) cc_final: 0.7341 (mt-10) REVERT: B 64 ASP cc_start: 0.8086 (t0) cc_final: 0.7867 (t0) REVERT: B 84 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 113 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6874 (t80) REVERT: B 306 LEU cc_start: 0.8503 (mt) cc_final: 0.8178 (mp) REVERT: B 341 LYS cc_start: 0.7774 (tptp) cc_final: 0.7065 (tptp) REVERT: B 526 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7865 (ttp80) REVERT: B 551 ASN cc_start: 0.7801 (m110) cc_final: 0.7527 (m-40) REVERT: C 59 ASP cc_start: 0.8196 (m-30) cc_final: 0.7815 (m-30) REVERT: C 84 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7290 (mm-30) REVERT: D 84 GLU cc_start: 0.7981 (tp30) cc_final: 0.7587 (tp30) REVERT: D 341 LYS cc_start: 0.7688 (tptt) cc_final: 0.7273 (tptt) REVERT: D 399 GLU cc_start: 0.8376 (tt0) cc_final: 0.8096 (tt0) REVERT: D 484 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8076 (mm-30) REVERT: D 544 ASN cc_start: 0.8793 (m110) cc_final: 0.8564 (m110) outliers start: 47 outliers final: 40 residues processed: 453 average time/residue: 0.2790 time to fit residues: 179.9223 Evaluate side-chains 472 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 431 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 13 ASN A 143 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 544 ASN C 10 ASN C 143 ASN D 5 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109999 restraints weight = 20561.750| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.55 r_work: 0.3246 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15068 Z= 0.135 Angle : 0.543 10.184 20244 Z= 0.286 Chirality : 0.043 0.137 2260 Planarity : 0.002 0.027 2572 Dihedral : 4.036 18.539 1952 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.88 % Allowed : 17.55 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1800 helix: 0.74 (0.23), residues: 576 sheet: 0.90 (0.26), residues: 444 loop : -2.06 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 126 HIS 0.004 0.001 HIS B 63 PHE 0.014 0.001 PHE D 315 TYR 0.015 0.001 TYR B 113 ARG 0.004 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 523) hydrogen bonds : angle 4.99050 ( 1497) covalent geometry : bond 0.00314 (15068) covalent geometry : angle 0.54319 (20244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 434 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7875 (t0) cc_final: 0.7645 (t0) REVERT: A 117 GLU cc_start: 0.7826 (tt0) cc_final: 0.7407 (tt0) REVERT: A 131 ASP cc_start: 0.8149 (m-30) cc_final: 0.7933 (m-30) REVERT: A 544 ASN cc_start: 0.8778 (m-40) cc_final: 0.8398 (m-40) REVERT: B 64 ASP cc_start: 0.8098 (t0) cc_final: 0.7884 (t0) REVERT: B 84 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7437 (mm-30) REVERT: B 113 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6886 (t80) REVERT: B 306 LEU cc_start: 0.8507 (mt) cc_final: 0.8174 (mp) REVERT: B 341 LYS cc_start: 0.7768 (tptp) cc_final: 0.7054 (tptp) REVERT: B 464 GLU cc_start: 0.8142 (mp0) cc_final: 0.7443 (mt-10) REVERT: B 526 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7834 (ttp80) REVERT: B 551 ASN cc_start: 0.7811 (m110) cc_final: 0.7535 (m-40) REVERT: C 84 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7288 (mm-30) REVERT: D 84 GLU cc_start: 0.7998 (tp30) cc_final: 0.7604 (tp30) REVERT: D 341 LYS cc_start: 0.7691 (tptt) cc_final: 0.7279 (tptt) REVERT: D 399 GLU cc_start: 0.8399 (tt0) cc_final: 0.8093 (tt0) REVERT: D 484 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8066 (mm-30) REVERT: D 544 ASN cc_start: 0.8793 (m110) cc_final: 0.8556 (m110) outliers start: 48 outliers final: 42 residues processed: 454 average time/residue: 0.2859 time to fit residues: 185.0597 Evaluate side-chains 474 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 431 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 143 ASN B 5 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 10 ASN C 143 ASN D 5 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108444 restraints weight = 20485.779| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.53 r_work: 0.3219 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15068 Z= 0.199 Angle : 0.598 9.785 20244 Z= 0.316 Chirality : 0.044 0.140 2260 Planarity : 0.003 0.041 2572 Dihedral : 4.217 19.726 1952 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 3.00 % Allowed : 17.67 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1800 helix: 0.58 (0.22), residues: 584 sheet: 0.83 (0.26), residues: 444 loop : -2.16 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 126 HIS 0.005 0.001 HIS B 63 PHE 0.019 0.002 PHE D 315 TYR 0.018 0.002 TYR B 113 ARG 0.005 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05492 ( 523) hydrogen bonds : angle 5.18089 ( 1497) covalent geometry : bond 0.00475 (15068) covalent geometry : angle 0.59787 (20244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 437 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7839 (t0) cc_final: 0.7634 (t0) REVERT: A 131 ASP cc_start: 0.8130 (m-30) cc_final: 0.7916 (m-30) REVERT: A 397 GLU cc_start: 0.7645 (pm20) cc_final: 0.7171 (pm20) REVERT: A 464 GLU cc_start: 0.7827 (mp0) cc_final: 0.7323 (mt-10) REVERT: A 539 LYS cc_start: 0.7922 (mptt) cc_final: 0.7716 (mmtt) REVERT: B 84 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 306 LEU cc_start: 0.8544 (mt) cc_final: 0.8224 (mp) REVERT: B 341 LYS cc_start: 0.7800 (tptp) cc_final: 0.7112 (tptp) REVERT: B 464 GLU cc_start: 0.8157 (mp0) cc_final: 0.7456 (mt-10) REVERT: B 526 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7880 (ttp80) REVERT: B 551 ASN cc_start: 0.7925 (m110) cc_final: 0.7566 (m-40) REVERT: C 59 ASP cc_start: 0.8225 (m-30) cc_final: 0.7848 (m-30) REVERT: C 84 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7282 (mm-30) REVERT: D 84 GLU cc_start: 0.8004 (tp30) cc_final: 0.7612 (tp30) REVERT: D 341 LYS cc_start: 0.7718 (tptt) cc_final: 0.7305 (tptt) REVERT: D 399 GLU cc_start: 0.8432 (tt0) cc_final: 0.8162 (tt0) REVERT: D 484 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8083 (mm-30) REVERT: D 544 ASN cc_start: 0.8823 (m110) cc_final: 0.8593 (m110) outliers start: 50 outliers final: 44 residues processed: 461 average time/residue: 0.2709 time to fit residues: 178.8646 Evaluate side-chains 477 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 433 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 176 optimal weight: 0.4980 chunk 171 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 13 ASN A 143 ASN B 5 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 461 ASN C 10 ASN C 143 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 143 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110161 restraints weight = 20494.341| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.54 r_work: 0.3242 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15068 Z= 0.137 Angle : 0.558 9.772 20244 Z= 0.294 Chirality : 0.043 0.163 2260 Planarity : 0.003 0.027 2572 Dihedral : 4.086 19.367 1952 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.76 % Allowed : 18.21 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1800 helix: 0.73 (0.23), residues: 584 sheet: 0.90 (0.26), residues: 444 loop : -2.09 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 126 HIS 0.004 0.001 HIS B 63 PHE 0.015 0.001 PHE D 315 TYR 0.012 0.001 TYR D 326 ARG 0.004 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 523) hydrogen bonds : angle 5.00968 ( 1497) covalent geometry : bond 0.00318 (15068) covalent geometry : angle 0.55840 (20244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 429 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7855 (t0) cc_final: 0.7604 (t70) REVERT: A 81 GLU cc_start: 0.7766 (pm20) cc_final: 0.7405 (pm20) REVERT: A 117 GLU cc_start: 0.7857 (tt0) cc_final: 0.7442 (tt0) REVERT: A 131 ASP cc_start: 0.8117 (m-30) cc_final: 0.7908 (m-30) REVERT: A 397 GLU cc_start: 0.7666 (pm20) cc_final: 0.7212 (pm20) REVERT: A 464 GLU cc_start: 0.7834 (mp0) cc_final: 0.7297 (mt-10) REVERT: A 544 ASN cc_start: 0.8778 (m-40) cc_final: 0.8372 (m-40) REVERT: B 84 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 306 LEU cc_start: 0.8514 (mt) cc_final: 0.8190 (mp) REVERT: B 341 LYS cc_start: 0.7780 (tptp) cc_final: 0.7067 (tptp) REVERT: B 464 GLU cc_start: 0.8174 (mp0) cc_final: 0.7452 (mt-10) REVERT: B 526 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7834 (ttp80) REVERT: B 551 ASN cc_start: 0.7812 (m110) cc_final: 0.7481 (m-40) REVERT: C 59 ASP cc_start: 0.8190 (m-30) cc_final: 0.7803 (m-30) REVERT: C 84 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7286 (mm-30) REVERT: D 84 GLU cc_start: 0.8011 (tp30) cc_final: 0.7620 (tp30) REVERT: D 341 LYS cc_start: 0.7669 (tptt) cc_final: 0.7243 (tptt) REVERT: D 399 GLU cc_start: 0.8436 (tt0) cc_final: 0.8093 (tt0) REVERT: D 484 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8068 (mm-30) REVERT: D 526 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7867 (ttp80) REVERT: D 544 ASN cc_start: 0.8789 (m110) cc_final: 0.8542 (m110) outliers start: 46 outliers final: 44 residues processed: 446 average time/residue: 0.2808 time to fit residues: 178.2454 Evaluate side-chains 472 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 428 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 39 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 148 optimal weight: 0.0670 chunk 146 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 5 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 10 ASN C 143 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110230 restraints weight = 20615.018| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.56 r_work: 0.3243 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 15068 Z= 0.200 Angle : 0.784 59.184 20244 Z= 0.458 Chirality : 0.051 1.291 2260 Planarity : 0.003 0.067 2572 Dihedral : 4.156 33.085 1952 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 2.94 % Allowed : 18.03 % Favored : 79.03 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1800 helix: 0.74 (0.23), residues: 584 sheet: 0.90 (0.26), residues: 444 loop : -2.09 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 126 HIS 0.004 0.001 HIS B 63 PHE 0.015 0.001 PHE D 315 TYR 0.011 0.001 TYR D 326 ARG 0.003 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 523) hydrogen bonds : angle 5.00941 ( 1497) covalent geometry : bond 0.00400 (15068) covalent geometry : angle 0.78359 (20244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8775.69 seconds wall clock time: 153 minutes 56.99 seconds (9236.99 seconds total)