Starting phenix.real_space_refine on Sat Oct 11 12:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tk0_41319/10_2025/8tk0_41319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tk0_41319/10_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_41319/10_2025/8tk0_41319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tk0_41319/10_2025/8tk0_41319.map" model { file = "/net/cci-nas-00/data/ceres_data/8tk0_41319/10_2025/8tk0_41319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tk0_41319/10_2025/8tk0_41319.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.67, per 1000 atoms: 0.25 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: 1.07 Conformation dependent library (CDL) restraints added in 668.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.60 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: 2.35 Time building geometry restraints manager: 1.48 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: 0.01 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: 18.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- 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 : 5.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (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 ARG 0.006 0.000 ARG B 332 TYR 0.030 0.002 TYR A 326 PHE 0.022 0.002 PHE C 53 TRP 0.101 0.019 TRP B 126 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00407 (15068) covalent geometry : angle 0.61424 (20244) hydrogen bonds : bond 0.21466 ( 523) hydrogen bonds : angle 7.26775 ( 1497) *********************** 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 : 0.598 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: 0.1350 time to fit residues: 97.7707 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 415 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111132 restraints weight = 20613.538| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.59 r_work: 0.3261 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1077 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= 0.130 Angle : 0.550 7.975 20244 Z= 0.293 Chirality : 0.043 0.141 2260 Planarity : 0.003 0.025 2572 Dihedral : 4.139 17.968 1952 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.08 % Allowed : 9.38 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1800 helix: 0.64 (0.23), residues: 576 sheet: 0.55 (0.25), residues: 460 loop : -2.13 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.018 0.002 TYR A 326 PHE 0.015 0.001 PHE C 315 TRP 0.053 0.010 TRP A 126 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00287 (15068) covalent geometry : angle 0.55049 (20244) hydrogen bonds : bond 0.04948 ( 523) hydrogen bonds : angle 5.36893 ( 1497) *********************** 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 474 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 456 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7820 (m-30) cc_final: 0.7594 (m-30) REVERT: A 289 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 306 LEU cc_start: 0.8201 (mt) cc_final: 0.7981 (mp) REVERT: A 367 SER cc_start: 0.8425 (p) cc_final: 0.8153 (p) REVERT: B 84 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 306 LEU cc_start: 0.8346 (mt) cc_final: 0.8052 (mp) REVERT: B 341 LYS cc_start: 0.7670 (tptp) cc_final: 0.6983 (tptp) REVERT: B 397 GLU cc_start: 0.7750 (pt0) cc_final: 0.7488 (pt0) REVERT: B 551 ASN cc_start: 0.7754 (m110) cc_final: 0.7372 (m-40) REVERT: C 84 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7163 (mm-30) REVERT: C 524 MET cc_start: 0.8055 (tpp) cc_final: 0.7731 (mmm) REVERT: D 84 GLU cc_start: 0.7845 (tp30) cc_final: 0.7443 (tp30) REVERT: D 135 ASP cc_start: 0.7276 (t0) cc_final: 0.6995 (t0) REVERT: D 341 LYS cc_start: 0.7584 (tptt) cc_final: 0.7251 (tptt) REVERT: D 367 SER cc_start: 0.8391 (p) cc_final: 0.8152 (p) REVERT: D 464 GLU cc_start: 0.7939 (mp0) cc_final: 0.7720 (mp0) REVERT: D 484 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7909 (mm-30) outliers start: 18 outliers final: 12 residues processed: 461 average time/residue: 0.1300 time to fit residues: 86.0414 Evaluate side-chains 456 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 444 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 434 ASP 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 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 164 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 121 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 A 455 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS C 10 ASN C 143 ASN D 10 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111236 restraints weight = 20800.507| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.58 r_work: 0.3259 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15068 Z= 0.127 Angle : 0.524 6.170 20244 Z= 0.279 Chirality : 0.043 0.137 2260 Planarity : 0.003 0.027 2572 Dihedral : 4.045 18.089 1952 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.80 % Allowed : 12.98 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1800 helix: 0.76 (0.23), residues: 580 sheet: 0.72 (0.26), residues: 452 loop : -2.09 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.014 0.001 TYR B 113 PHE 0.015 0.001 PHE A 315 TRP 0.041 0.007 TRP A 126 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00288 (15068) covalent geometry : angle 0.52352 (20244) hydrogen bonds : bond 0.04665 ( 523) hydrogen bonds : angle 5.11999 ( 1497) *********************** 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 466 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 436 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7813 (m-30) cc_final: 0.7591 (m-30) REVERT: A 289 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 306 LEU cc_start: 0.8242 (mt) cc_final: 0.7990 (mp) REVERT: A 565 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8589 (mttt) REVERT: B 84 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 306 LEU cc_start: 0.8383 (mt) cc_final: 0.8090 (mp) REVERT: B 341 LYS cc_start: 0.7666 (tptp) cc_final: 0.7010 (tptp) REVERT: B 355 TYR cc_start: 0.7877 (m-10) cc_final: 0.7256 (m-10) REVERT: B 397 GLU cc_start: 0.7743 (pt0) cc_final: 0.7480 (pt0) REVERT: B 551 ASN cc_start: 0.7681 (m110) cc_final: 0.7348 (m-40) REVERT: C 84 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7135 (mm-30) REVERT: D 67 LYS cc_start: 0.8655 (mttp) cc_final: 0.8375 (mttp) REVERT: D 84 GLU cc_start: 0.7841 (tp30) cc_final: 0.7449 (tp30) REVERT: D 135 ASP cc_start: 0.7227 (t0) cc_final: 0.6978 (t0) REVERT: D 484 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7901 (mm-30) outliers start: 30 outliers final: 19 residues processed: 448 average time/residue: 0.1361 time to fit residues: 87.7360 Evaluate side-chains 444 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 425 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN 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 343 VAL Chi-restraints excluded: chain B residue 507 LEU 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 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 179 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 295 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110600 restraints weight = 20601.906| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.56 r_work: 0.3246 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15068 Z= 0.132 Angle : 0.520 6.155 20244 Z= 0.278 Chirality : 0.043 0.135 2260 Planarity : 0.002 0.027 2572 Dihedral : 4.028 18.079 1952 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.40 % Allowed : 14.24 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1800 helix: 0.87 (0.23), residues: 576 sheet: 0.75 (0.26), residues: 452 loop : -2.10 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.017 0.001 TYR B 113 PHE 0.016 0.001 PHE A 315 TRP 0.035 0.006 TRP D 126 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00303 (15068) covalent geometry : angle 0.51967 (20244) hydrogen bonds : bond 0.04592 ( 523) hydrogen bonds : angle 5.03198 ( 1497) *********************** 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 473 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 433 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7789 (t0) cc_final: 0.7538 (t0) REVERT: A 131 ASP cc_start: 0.7817 (m-30) cc_final: 0.7590 (m-30) REVERT: A 289 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 306 LEU cc_start: 0.8244 (mt) cc_final: 0.7993 (mp) REVERT: A 565 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8630 (mttt) REVERT: B 84 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 306 LEU cc_start: 0.8400 (mt) cc_final: 0.8103 (mp) REVERT: B 341 LYS cc_start: 0.7666 (tptp) cc_final: 0.7012 (tptp) REVERT: B 355 TYR cc_start: 0.7916 (m-10) cc_final: 0.7341 (m-10) REVERT: B 397 GLU cc_start: 0.7778 (pt0) cc_final: 0.7519 (pt0) REVERT: B 526 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7682 (ttp80) REVERT: B 551 ASN cc_start: 0.7702 (m110) cc_final: 0.7420 (m-40) REVERT: C 84 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7127 (mm-30) REVERT: C 524 MET cc_start: 0.8071 (tpp) cc_final: 0.7760 (mmm) REVERT: D 84 GLU cc_start: 0.7842 (tp30) cc_final: 0.7456 (tp30) REVERT: D 135 ASP cc_start: 0.7235 (t0) cc_final: 0.7016 (t0) REVERT: D 341 LYS cc_start: 0.7590 (tptt) cc_final: 0.7174 (tptt) REVERT: D 484 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7867 (mm-30) outliers start: 40 outliers final: 28 residues processed: 449 average time/residue: 0.1374 time to fit residues: 88.7687 Evaluate side-chains 458 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 430 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 439 LYS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain B residue 30 MET 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 378 ILE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE 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 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 30 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 131 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 143 ASN B 5 ASN B 10 ASN B 25 ASN B 143 ASN B 415 HIS C 10 ASN C 143 ASN D 5 ASN D 10 ASN D 25 ASN D 141 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112118 restraints weight = 20700.912| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.57 r_work: 0.3275 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15068 Z= 0.100 Angle : 0.490 6.197 20244 Z= 0.261 Chirality : 0.042 0.136 2260 Planarity : 0.002 0.023 2572 Dihedral : 3.883 17.625 1952 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.52 % Allowed : 14.78 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.20), residues: 1800 helix: 0.83 (0.23), residues: 592 sheet: 0.82 (0.26), residues: 452 loop : -2.02 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.014 0.001 TYR B 113 PHE 0.012 0.001 PHE A 315 TRP 0.026 0.004 TRP D 126 HIS 0.003 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00220 (15068) covalent geometry : angle 0.49036 (20244) hydrogen bonds : bond 0.03768 ( 523) hydrogen bonds : angle 4.84067 ( 1497) *********************** 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 469 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 427 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7800 (m-30) cc_final: 0.7574 (m-30) REVERT: A 289 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 306 LEU cc_start: 0.8184 (mt) cc_final: 0.7943 (mp) REVERT: A 539 LYS cc_start: 0.7864 (mptt) cc_final: 0.7656 (mptt) REVERT: A 565 LYS cc_start: 0.8840 (mmtp) cc_final: 0.8612 (mttt) REVERT: B 84 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 306 LEU cc_start: 0.8361 (mt) cc_final: 0.8060 (mp) REVERT: B 341 LYS cc_start: 0.7642 (tptp) cc_final: 0.6971 (tptp) REVERT: B 355 TYR cc_start: 0.7904 (m-10) cc_final: 0.7288 (m-10) REVERT: B 397 GLU cc_start: 0.7786 (pt0) cc_final: 0.7530 (pt0) REVERT: B 526 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7670 (ttp80) REVERT: C 59 ASP cc_start: 0.8054 (m-30) cc_final: 0.7682 (m-30) REVERT: C 84 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7108 (mm-30) REVERT: C 464 GLU cc_start: 0.7982 (mp0) cc_final: 0.7765 (mp0) REVERT: D 68 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8185 (mtpt) REVERT: D 84 GLU cc_start: 0.7815 (tp30) cc_final: 0.7419 (tp30) REVERT: D 341 LYS cc_start: 0.7564 (tptt) cc_final: 0.7175 (tptt) REVERT: D 484 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7848 (mm-30) REVERT: D 544 ASN cc_start: 0.8669 (m110) cc_final: 0.8449 (m110) outliers start: 42 outliers final: 33 residues processed: 444 average time/residue: 0.1362 time to fit residues: 86.2957 Evaluate side-chains 459 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 426 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 463 ASP 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 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 B residue 507 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 122 ILE 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 25 ASN Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 406 LEU 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 132 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 141 ASN A 143 ASN A 455 ASN B 25 ASN C 10 ASN D 5 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.128115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110135 restraints weight = 20556.177| |-----------------------------------------------------------------------------| 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: 0.3084 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15068 Z= 0.149 Angle : 0.529 8.376 20244 Z= 0.280 Chirality : 0.043 0.135 2260 Planarity : 0.002 0.031 2572 Dihedral : 3.969 18.355 1952 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.82 % Allowed : 15.50 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.20), residues: 1800 helix: 0.84 (0.23), residues: 576 sheet: 0.92 (0.26), residues: 444 loop : -2.02 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.015 0.001 TYR B 113 PHE 0.018 0.002 PHE A 315 TRP 0.024 0.004 TRP D 126 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00350 (15068) covalent geometry : angle 0.52890 (20244) hydrogen bonds : bond 0.04701 ( 523) hydrogen bonds : angle 4.95972 ( 1497) *********************** 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 481 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 434 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8125 (m-30) cc_final: 0.7904 (m-30) REVERT: A 289 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 306 LEU cc_start: 0.8322 (mt) cc_final: 0.8043 (mp) REVERT: B 64 ASP cc_start: 0.7980 (t0) cc_final: 0.7648 (t0) REVERT: B 84 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 306 LEU cc_start: 0.8501 (mt) cc_final: 0.8179 (mp) REVERT: B 341 LYS cc_start: 0.7762 (tptp) cc_final: 0.7055 (tptp) REVERT: B 397 GLU cc_start: 0.8080 (pt0) cc_final: 0.7837 (pt0) REVERT: B 526 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7816 (ttp80) REVERT: B 551 ASN cc_start: 0.7796 (m110) cc_final: 0.7514 (m-40) REVERT: C 84 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7309 (mm-30) REVERT: D 68 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8321 (mtpt) REVERT: D 84 GLU cc_start: 0.7966 (tp30) cc_final: 0.7580 (tp30) REVERT: D 341 LYS cc_start: 0.7681 (tptt) cc_final: 0.7267 (tptt) REVERT: D 484 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8067 (mm-30) outliers start: 47 outliers final: 39 residues processed: 460 average time/residue: 0.1263 time to fit residues: 84.0886 Evaluate side-chains 457 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 418 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 367 SER 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 463 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 378 ILE 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 57 LYS 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 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 91 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 39 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 0.0050 chunk 158 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.4912 ------------------------------------------------------------------------------- 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 C 10 ASN D 5 ASN D 10 ASN D 25 ASN D 141 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111956 restraints weight = 20451.735| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.56 r_work: 0.3275 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15068 Z= 0.102 Angle : 0.500 7.128 20244 Z= 0.265 Chirality : 0.042 0.135 2260 Planarity : 0.002 0.022 2572 Dihedral : 3.875 18.009 1952 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.00 % Allowed : 15.93 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.20), residues: 1800 helix: 0.87 (0.23), residues: 592 sheet: 1.01 (0.26), residues: 444 loop : -2.01 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.012 0.001 TYR B 113 PHE 0.013 0.001 PHE A 315 TRP 0.018 0.003 TRP D 126 HIS 0.003 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00226 (15068) covalent geometry : angle 0.49963 (20244) hydrogen bonds : bond 0.03784 ( 523) hydrogen bonds : angle 4.81612 ( 1497) *********************** 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 470 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 420 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7794 (tt0) cc_final: 0.7384 (tt0) REVERT: A 131 ASP cc_start: 0.8130 (m-30) cc_final: 0.7909 (m-30) REVERT: A 306 LEU cc_start: 0.8255 (mt) cc_final: 0.7986 (mp) REVERT: A 341 LYS cc_start: 0.7362 (mmmt) cc_final: 0.7102 (mmmt) REVERT: A 464 GLU cc_start: 0.7815 (mp0) cc_final: 0.7262 (mt-10) REVERT: A 539 LYS cc_start: 0.7929 (mptt) cc_final: 0.7693 (mptt) REVERT: B 84 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 306 LEU cc_start: 0.8463 (mt) cc_final: 0.8162 (mp) REVERT: B 341 LYS cc_start: 0.7742 (tptp) cc_final: 0.7029 (tptp) REVERT: B 397 GLU cc_start: 0.8053 (pt0) cc_final: 0.7806 (pt0) REVERT: B 526 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7789 (ttp80) REVERT: C 84 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7292 (mm-30) REVERT: D 68 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8324 (mtpt) REVERT: D 84 GLU cc_start: 0.7934 (tp30) cc_final: 0.7543 (tp30) REVERT: D 341 LYS cc_start: 0.7656 (tptt) cc_final: 0.7230 (tptt) REVERT: D 464 GLU cc_start: 0.7700 (mp0) cc_final: 0.7438 (mp0) REVERT: D 484 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8040 (mm-30) REVERT: D 544 ASN cc_start: 0.8775 (m110) cc_final: 0.8509 (m110) outliers start: 50 outliers final: 43 residues processed: 442 average time/residue: 0.1358 time to fit residues: 85.8304 Evaluate side-chains 467 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 424 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 320 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 367 SER 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 463 ASP 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 320 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 378 ILE 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 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 25 ASN Chi-restraints excluded: chain D residue 57 LYS 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 480 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 510 ILE 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 56 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 143 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS C 10 ASN C 143 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110675 restraints weight = 20585.359| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.55 r_work: 0.3254 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15068 Z= 0.137 Angle : 0.533 9.615 20244 Z= 0.281 Chirality : 0.043 0.136 2260 Planarity : 0.002 0.028 2572 Dihedral : 3.932 18.192 1952 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.12 % Allowed : 16.47 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.20), residues: 1800 helix: 0.90 (0.23), residues: 584 sheet: 0.99 (0.26), residues: 444 loop : -2.05 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.014 0.001 TYR B 113 PHE 0.017 0.001 PHE D 315 TRP 0.017 0.003 TRP D 126 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00317 (15068) covalent geometry : angle 0.53255 (20244) hydrogen bonds : bond 0.04399 ( 523) hydrogen bonds : angle 4.88437 ( 1497) *********************** 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 471 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8141 (m-30) cc_final: 0.7917 (m-30) REVERT: A 306 LEU cc_start: 0.8297 (mt) cc_final: 0.8019 (mp) REVERT: A 464 GLU cc_start: 0.7814 (mp0) cc_final: 0.7263 (mt-10) REVERT: B 84 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 306 LEU cc_start: 0.8501 (mt) cc_final: 0.8174 (mp) REVERT: B 341 LYS cc_start: 0.7754 (tptp) cc_final: 0.7048 (tptp) REVERT: B 397 GLU cc_start: 0.8066 (pt0) cc_final: 0.7820 (pt0) REVERT: B 464 GLU cc_start: 0.8117 (mp0) cc_final: 0.7425 (mt-10) REVERT: C 84 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7311 (mm-30) REVERT: D 68 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8292 (mtpt) REVERT: D 84 GLU cc_start: 0.7940 (tp30) cc_final: 0.7556 (tp30) REVERT: D 341 LYS cc_start: 0.7650 (tptt) cc_final: 0.7246 (tptt) REVERT: D 484 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8064 (mm-30) REVERT: D 544 ASN cc_start: 0.8793 (m110) cc_final: 0.8528 (m110) outliers start: 52 outliers final: 48 residues processed: 441 average time/residue: 0.1258 time to fit residues: 79.9774 Evaluate side-chains 464 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 416 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 463 ASP 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 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 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 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 57 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 357 SER 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 480 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 510 ILE 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 178 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 143 ASN B 5 ASN B 10 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN C 143 ASN D 5 ASN D 10 ASN D 25 ASN D 141 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109116 restraints weight = 20708.541| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.55 r_work: 0.3225 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15068 Z= 0.190 Angle : 0.579 7.262 20244 Z= 0.306 Chirality : 0.044 0.140 2260 Planarity : 0.003 0.040 2572 Dihedral : 4.142 19.515 1952 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.19 % Allowed : 16.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.20), residues: 1800 helix: 0.76 (0.23), residues: 576 sheet: 0.92 (0.26), residues: 444 loop : -2.05 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 332 TYR 0.018 0.002 TYR B 113 PHE 0.019 0.002 PHE A 315 TRP 0.017 0.003 TRP D 126 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00453 (15068) covalent geometry : angle 0.57909 (20244) hydrogen bonds : bond 0.05341 ( 523) hydrogen bonds : angle 5.10341 ( 1497) *********************** 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 491 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 438 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8157 (m-30) cc_final: 0.7936 (m-30) REVERT: A 306 LEU cc_start: 0.8352 (mt) cc_final: 0.8066 (mp) REVERT: A 464 GLU cc_start: 0.7837 (mp0) cc_final: 0.7293 (mt-10) REVERT: B 84 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 306 LEU cc_start: 0.8537 (mt) cc_final: 0.8219 (mp) REVERT: B 341 LYS cc_start: 0.7791 (tptp) cc_final: 0.7092 (tptp) REVERT: B 526 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7834 (ttp80) REVERT: B 551 ASN cc_start: 0.7899 (m110) cc_final: 0.7578 (m-40) REVERT: C 59 ASP cc_start: 0.8216 (m-30) cc_final: 0.7855 (m-30) REVERT: C 84 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 464 GLU cc_start: 0.8150 (mp0) cc_final: 0.7870 (mp0) REVERT: D 68 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8302 (mtpt) REVERT: D 84 GLU cc_start: 0.7962 (tp30) cc_final: 0.7578 (tp30) REVERT: D 341 LYS cc_start: 0.7700 (tptt) cc_final: 0.7285 (tptt) REVERT: D 484 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8088 (mm-30) outliers start: 53 outliers final: 47 residues processed: 455 average time/residue: 0.1326 time to fit residues: 86.9770 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 : 0.623 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 353 GLU 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 463 ASP 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 50 ILE 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 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 283 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 357 SER 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 480 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 510 ILE 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 10 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 415 HIS C 10 ASN C 143 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110569 restraints weight = 20758.312| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.51 r_work: 0.3245 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1855 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= 0.131 Angle : 0.559 11.228 20244 Z= 0.293 Chirality : 0.043 0.138 2260 Planarity : 0.003 0.027 2572 Dihedral : 4.047 19.164 1952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.94 % Allowed : 16.89 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.20), residues: 1800 helix: 0.88 (0.23), residues: 584 sheet: 0.96 (0.26), residues: 444 loop : -2.09 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 12 TYR 0.015 0.001 TYR B 113 PHE 0.015 0.001 PHE A 315 TRP 0.015 0.003 TRP D 126 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00304 (15068) covalent geometry : angle 0.55895 (20244) hydrogen bonds : bond 0.04387 ( 523) hydrogen bonds : angle 4.97746 ( 1497) ********************** 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 464 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 415 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8067 (m-30) cc_final: 0.7852 (m-30) REVERT: A 306 LEU cc_start: 0.8311 (mt) cc_final: 0.8019 (mp) REVERT: A 464 GLU cc_start: 0.7804 (mp0) cc_final: 0.7284 (mt-10) REVERT: B 84 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 306 LEU cc_start: 0.8540 (mt) cc_final: 0.8199 (mp) REVERT: B 341 LYS cc_start: 0.7776 (tptp) cc_final: 0.7056 (tptp) REVERT: B 464 GLU cc_start: 0.8129 (mp0) cc_final: 0.7410 (mt-10) REVERT: B 526 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7751 (ttp80) REVERT: B 551 ASN cc_start: 0.7807 (m110) cc_final: 0.7509 (m-40) REVERT: C 84 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7317 (mm-30) REVERT: C 464 GLU cc_start: 0.8147 (mp0) cc_final: 0.7898 (mp0) REVERT: D 68 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8302 (mtpt) REVERT: D 84 GLU cc_start: 0.7910 (tp30) cc_final: 0.7524 (tp30) REVERT: D 341 LYS cc_start: 0.7666 (tptt) cc_final: 0.7244 (tptt) REVERT: D 464 GLU cc_start: 0.7725 (mp0) cc_final: 0.7440 (mp0) REVERT: D 484 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 526 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7894 (ttp80) outliers start: 49 outliers final: 47 residues processed: 437 average time/residue: 0.1384 time to fit residues: 87.1242 Evaluate side-chains 460 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 413 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 367 SER 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 463 ASP 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 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 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 537 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 57 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 357 SER 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 480 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 510 ILE 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 6 optimal weight: 0.0070 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 155 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 143 ASN C 10 ASN C 143 ASN D 5 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 = 0.3651 r_free = 0.3651 target = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112114 restraints weight = 20697.680| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.50 r_work: 0.3269 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15068 Z= 0.102 Angle : 0.539 10.774 20244 Z= 0.282 Chirality : 0.042 0.135 2260 Planarity : 0.002 0.025 2572 Dihedral : 3.892 18.815 1952 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.88 % Allowed : 16.95 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.20), residues: 1800 helix: 0.92 (0.23), residues: 592 sheet: 1.01 (0.26), residues: 444 loop : -2.03 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.012 0.001 TYR B 113 PHE 0.012 0.001 PHE A 315 TRP 0.014 0.002 TRP D 126 HIS 0.003 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00226 (15068) covalent geometry : angle 0.53879 (20244) hydrogen bonds : bond 0.03637 ( 523) hydrogen bonds : angle 4.81458 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.69 seconds wall clock time: 73 minutes 19.96 seconds (4399.96 seconds total)