Starting phenix.real_space_refine on Sat May 24 12:32:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t15_40955/05_2025/8t15_40955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t15_40955/05_2025/8t15_40955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t15_40955/05_2025/8t15_40955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t15_40955/05_2025/8t15_40955.map" model { file = "/net/cci-nas-00/data/ceres_data/8t15_40955/05_2025/8t15_40955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t15_40955/05_2025/8t15_40955.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 8256 2.51 5 N 2340 2.21 5 O 2388 1.98 5 H 12612 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "B" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "C" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "E" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "F" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "G" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "I" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "J" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "K" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Time building chain proxies: 12.85, per 1000 atoms: 0.50 Number of scatterers: 25656 At special positions: 0 Unit cell: (120.783, 125.229, 70.395, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 O 2388 8.00 N 2340 7.00 C 8256 6.00 H 12612 1.00 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: 6.67 Conformation dependent library (CDL) restraints added in 2.9 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 31.4% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 345 through 363 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 392 through 402 removed outlier: 4.019A pdb=" N PHE B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 392 through 402 removed outlier: 4.017A pdb=" N PHE C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR C 398 " --> pdb=" O PHE C 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 363 Processing helix chain 'D' and resid 365 through 372 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE E 350 " --> pdb=" O ARG E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 392 through 402 removed outlier: 4.021A pdb=" N PHE E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 363 Processing helix chain 'F' and resid 365 through 372 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 392 through 402 removed outlier: 4.017A pdb=" N PHE F 397 " --> pdb=" O ASP F 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 363 Processing helix chain 'G' and resid 365 through 372 Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'G' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE H 350 " --> pdb=" O ARG H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 372 Processing helix chain 'H' and resid 381 through 385 Processing helix chain 'H' and resid 392 through 402 removed outlier: 4.019A pdb=" N PHE H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 363 Processing helix chain 'I' and resid 365 through 372 Processing helix chain 'I' and resid 381 through 385 Processing helix chain 'I' and resid 392 through 402 removed outlier: 4.017A pdb=" N PHE I 397 " --> pdb=" O ASP I 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 363 Processing helix chain 'J' and resid 365 through 372 Processing helix chain 'J' and resid 381 through 385 Processing helix chain 'J' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE J 397 " --> pdb=" O ASP J 393 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR J 398 " --> pdb=" O PHE J 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 372 Processing helix chain 'K' and resid 381 through 385 Processing helix chain 'K' and resid 392 through 402 removed outlier: 4.018A pdb=" N PHE K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR K 398 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 363 Processing helix chain 'L' and resid 365 through 372 Processing helix chain 'L' and resid 381 through 385 Processing helix chain 'L' and resid 392 through 402 removed outlier: 4.018A pdb=" N PHE L 397 " --> pdb=" O ASP L 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR L 398 " --> pdb=" O PHE L 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390 removed outlier: 8.917A pdb=" N ASP A 374 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN A 463 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLY A 376 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 465 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 454 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 467 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 452 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG A 469 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A 450 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY A 471 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN A 448 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER A 426 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU A 421 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 428 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 419 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 430 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP B 374 " --> pdb=" O LYS B 461 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N GLN B 463 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N GLY B 376 " --> pdb=" O GLN B 463 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 465 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 454 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE B 467 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 452 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG B 469 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 450 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY B 471 " --> pdb=" O GLN B 448 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLN B 448 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER B 426 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU B 421 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 428 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 419 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 430 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 389 through 390 removed outlier: 8.929A pdb=" N ASP C 374 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN C 463 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLY C 376 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 465 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 454 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE C 467 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 452 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG C 469 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU C 450 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY C 471 " --> pdb=" O GLN C 448 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN C 448 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER C 426 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU C 421 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS C 428 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE C 419 " --> pdb=" O CYS C 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 430 " --> pdb=" O PRO C 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 389 through 390 removed outlier: 8.917A pdb=" N ASP D 374 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN D 463 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLY D 376 " --> pdb=" O GLN D 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL D 465 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 454 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE D 467 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 452 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 469 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU D 450 " --> pdb=" O ARG D 469 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY D 471 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLN D 448 " --> pdb=" O GLY D 471 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER D 426 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU D 421 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS D 428 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE D 419 " --> pdb=" O CYS D 428 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 430 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP E 374 " --> pdb=" O LYS E 461 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLN E 463 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N GLY E 376 " --> pdb=" O GLN E 463 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 465 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL E 454 " --> pdb=" O VAL E 465 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E 467 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR E 452 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG E 469 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU E 450 " --> pdb=" O ARG E 469 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY E 471 " --> pdb=" O GLN E 448 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLN E 448 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N SER E 426 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU E 421 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS E 428 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE E 419 " --> pdb=" O CYS E 428 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA E 430 " --> pdb=" O PRO E 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 389 through 390 removed outlier: 8.927A pdb=" N ASP F 374 " --> pdb=" O LYS F 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN F 463 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLY F 376 " --> pdb=" O GLN F 463 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL F 465 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL F 454 " --> pdb=" O VAL F 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE F 467 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR F 452 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG F 469 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU F 450 " --> pdb=" O ARG F 469 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY F 471 " --> pdb=" O GLN F 448 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN F 448 " --> pdb=" O GLY F 471 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER F 426 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU F 421 " --> pdb=" O SER F 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS F 428 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE F 419 " --> pdb=" O CYS F 428 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA F 430 " --> pdb=" O PRO F 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 389 through 390 removed outlier: 8.917A pdb=" N ASP G 374 " --> pdb=" O LYS G 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN G 463 " --> pdb=" O ASP G 374 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLY G 376 " --> pdb=" O GLN G 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL G 465 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL G 454 " --> pdb=" O VAL G 465 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE G 467 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR G 452 " --> pdb=" O PHE G 467 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG G 469 " --> pdb=" O GLU G 450 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 450 " --> pdb=" O ARG G 469 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 471 " --> pdb=" O GLN G 448 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN G 448 " --> pdb=" O GLY G 471 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER G 426 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU G 421 " --> pdb=" O SER G 426 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS G 428 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE G 419 " --> pdb=" O CYS G 428 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA G 430 " --> pdb=" O PRO G 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP H 374 " --> pdb=" O LYS H 461 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N GLN H 463 " --> pdb=" O ASP H 374 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N GLY H 376 " --> pdb=" O GLN H 463 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL H 465 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL H 454 " --> pdb=" O VAL H 465 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE H 467 " --> pdb=" O THR H 452 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR H 452 " --> pdb=" O PHE H 467 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG H 469 " --> pdb=" O GLU H 450 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU H 450 " --> pdb=" O ARG H 469 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY H 471 " --> pdb=" O GLN H 448 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN H 448 " --> pdb=" O GLY H 471 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER H 426 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU H 421 " --> pdb=" O SER H 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS H 428 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE H 419 " --> pdb=" O CYS H 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA H 430 " --> pdb=" O PRO H 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 389 through 390 removed outlier: 8.929A pdb=" N ASP I 374 " --> pdb=" O LYS I 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN I 463 " --> pdb=" O ASP I 374 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLY I 376 " --> pdb=" O GLN I 463 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL I 465 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL I 454 " --> pdb=" O VAL I 465 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE I 467 " --> pdb=" O THR I 452 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR I 452 " --> pdb=" O PHE I 467 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG I 469 " --> pdb=" O GLU I 450 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU I 450 " --> pdb=" O ARG I 469 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY I 471 " --> pdb=" O GLN I 448 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN I 448 " --> pdb=" O GLY I 471 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER I 426 " --> pdb=" O LEU I 421 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU I 421 " --> pdb=" O SER I 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS I 428 " --> pdb=" O ILE I 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE I 419 " --> pdb=" O CYS I 428 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA I 430 " --> pdb=" O PRO I 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 389 through 390 removed outlier: 8.916A pdb=" N ASP J 374 " --> pdb=" O LYS J 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN J 463 " --> pdb=" O ASP J 374 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLY J 376 " --> pdb=" O GLN J 463 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL J 465 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL J 454 " --> pdb=" O VAL J 465 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE J 467 " --> pdb=" O THR J 452 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR J 452 " --> pdb=" O PHE J 467 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG J 469 " --> pdb=" O GLU J 450 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU J 450 " --> pdb=" O ARG J 469 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY J 471 " --> pdb=" O GLN J 448 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN J 448 " --> pdb=" O GLY J 471 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER J 426 " --> pdb=" O LEU J 421 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU J 421 " --> pdb=" O SER J 426 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS J 428 " --> pdb=" O ILE J 419 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE J 419 " --> pdb=" O CYS J 428 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA J 430 " --> pdb=" O PRO J 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP K 374 " --> pdb=" O LYS K 461 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN K 463 " --> pdb=" O ASP K 374 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLY K 376 " --> pdb=" O GLN K 463 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL K 465 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL K 454 " --> pdb=" O VAL K 465 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE K 467 " --> pdb=" O THR K 452 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR K 452 " --> pdb=" O PHE K 467 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG K 469 " --> pdb=" O GLU K 450 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU K 450 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY K 471 " --> pdb=" O GLN K 448 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLN K 448 " --> pdb=" O GLY K 471 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER K 426 " --> pdb=" O LEU K 421 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU K 421 " --> pdb=" O SER K 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS K 428 " --> pdb=" O ILE K 419 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE K 419 " --> pdb=" O CYS K 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA K 430 " --> pdb=" O PRO K 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 389 through 390 removed outlier: 8.928A pdb=" N ASP L 374 " --> pdb=" O LYS L 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN L 463 " --> pdb=" O ASP L 374 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLY L 376 " --> pdb=" O GLN L 463 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL L 465 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL L 454 " --> pdb=" O VAL L 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE L 467 " --> pdb=" O THR L 452 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR L 452 " --> pdb=" O PHE L 467 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG L 469 " --> pdb=" O GLU L 450 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU L 450 " --> pdb=" O ARG L 469 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY L 471 " --> pdb=" O GLN L 448 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN L 448 " --> pdb=" O GLY L 471 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER L 426 " --> pdb=" O LEU L 421 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU L 421 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS L 428 " --> pdb=" O ILE L 419 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE L 419 " --> pdb=" O CYS L 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA L 430 " --> pdb=" O PRO L 417 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1755 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: 9.04 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12588 1.03 - 1.23: 24 1.23 - 1.42: 5856 1.42 - 1.61: 7452 1.61 - 1.81: 96 Bond restraints: 26016 Sorted by residual: bond pdb=" N VAL L 345 " pdb=" CA VAL L 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N VAL B 345 " pdb=" CA VAL B 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N VAL K 345 " pdb=" CA VAL K 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N VAL E 345 " pdb=" CA VAL E 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N VAL C 345 " pdb=" CA VAL C 345 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 ... (remaining 26011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 42345 0.91 - 1.81: 4153 1.81 - 2.72: 223 2.72 - 3.63: 87 3.63 - 4.53: 28 Bond angle restraints: 46836 Sorted by residual: angle pdb=" N VAL C 465 " pdb=" CA VAL C 465 " pdb=" C VAL C 465 " ideal model delta sigma weight residual 111.90 109.63 2.27 8.10e-01 1.52e+00 7.84e+00 angle pdb=" N VAL E 465 " pdb=" CA VAL E 465 " pdb=" C VAL E 465 " ideal model delta sigma weight residual 111.90 109.69 2.21 8.10e-01 1.52e+00 7.42e+00 angle pdb=" N VAL I 465 " pdb=" CA VAL I 465 " pdb=" C VAL I 465 " ideal model delta sigma weight residual 111.90 109.70 2.20 8.10e-01 1.52e+00 7.38e+00 angle pdb=" N VAL F 465 " pdb=" CA VAL F 465 " pdb=" C VAL F 465 " ideal model delta sigma weight residual 111.90 109.70 2.20 8.10e-01 1.52e+00 7.38e+00 angle pdb=" N VAL L 465 " pdb=" CA VAL L 465 " pdb=" C VAL L 465 " ideal model delta sigma weight residual 111.90 109.70 2.20 8.10e-01 1.52e+00 7.37e+00 ... (remaining 46831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 11071 17.06 - 34.12: 696 34.12 - 51.18: 374 51.18 - 68.24: 120 68.24 - 85.30: 39 Dihedral angle restraints: 12300 sinusoidal: 6588 harmonic: 5712 Sorted by residual: dihedral pdb=" CA ALA E 379 " pdb=" C ALA E 379 " pdb=" N PHE E 380 " pdb=" CA PHE E 380 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA F 379 " pdb=" C ALA F 379 " pdb=" N PHE F 380 " pdb=" CA PHE F 380 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA C 379 " pdb=" C ALA C 379 " pdb=" N PHE C 380 " pdb=" CA PHE C 380 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1058 0.027 - 0.053: 537 0.053 - 0.080: 161 0.080 - 0.106: 69 0.106 - 0.133: 95 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA VAL L 345 " pdb=" N VAL L 345 " pdb=" C VAL L 345 " pdb=" CB VAL L 345 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B 345 " pdb=" N VAL B 345 " pdb=" C VAL B 345 " pdb=" CB VAL B 345 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1917 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 472 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.87e-01 pdb=" N PRO H 473 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO H 473 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 473 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 472 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.82e-01 pdb=" N PRO E 473 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 473 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 473 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " 0.016 5.00e-02 4.00e+02 2.47e-02 9.76e-01 pdb=" N PRO B 473 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " 0.014 5.00e-02 4.00e+02 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 5240 2.30 - 2.88: 55609 2.88 - 3.45: 64245 3.45 - 4.03: 94103 4.03 - 4.60: 138564 Nonbonded interactions: 357761 Sorted by model distance: nonbonded pdb=" O ILE H 350 " pdb=" HG1 THR H 354 " model vdw 1.727 2.450 nonbonded pdb=" O ILE B 350 " pdb=" HG1 THR B 354 " model vdw 1.727 2.450 nonbonded pdb=" O ILE K 350 " pdb=" HG1 THR K 354 " model vdw 1.727 2.450 nonbonded pdb=" O ILE E 350 " pdb=" HG1 THR E 354 " model vdw 1.728 2.450 nonbonded pdb=" O ILE L 350 " pdb=" HG1 THR L 354 " model vdw 1.733 2.450 ... (remaining 357756 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.550 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: 0.470 Extract box with map and model: 1.110 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.210 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.002 0.032 13404 Z= 0.138 Angle : 0.533 4.431 18180 Z= 0.319 Chirality : 0.044 0.133 1920 Planarity : 0.004 0.033 2376 Dihedral : 16.278 85.302 4920 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.21), residues: 1584 helix: 0.86 (0.25), residues: 408 sheet: 3.25 (0.21), residues: 552 loop : -0.59 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 455 HIS 0.002 0.000 HIS H 420 PHE 0.013 0.002 PHE K 467 TYR 0.005 0.001 TYR K 398 ARG 0.004 0.000 ARG G 396 Details of bonding type rmsd hydrogen bonds : bond 0.15570 ( 645) hydrogen bonds : angle 5.25980 ( 1755) covalent geometry : bond 0.00248 (13404) covalent geometry : angle 0.53254 (18180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 2.233 Fit side-chains REVERT: H 424 ASP cc_start: 0.8276 (p0) cc_final: 0.8007 (m-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 4.2314 time to fit residues: 967.3294 Evaluate side-chains 198 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132431 restraints weight = 33430.554| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.93 r_work: 0.3380 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13404 Z= 0.191 Angle : 0.561 3.884 18180 Z= 0.317 Chirality : 0.046 0.154 1920 Planarity : 0.005 0.028 2376 Dihedral : 4.571 21.665 1764 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.28 % Allowed : 12.75 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1584 helix: 0.38 (0.24), residues: 456 sheet: 2.97 (0.21), residues: 552 loop : -0.71 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 455 HIS 0.004 0.001 HIS K 468 PHE 0.014 0.002 PHE H 467 TYR 0.009 0.002 TYR B 398 ARG 0.004 0.001 ARG I 405 Details of bonding type rmsd hydrogen bonds : bond 0.05812 ( 645) hydrogen bonds : angle 4.95700 ( 1755) covalent geometry : bond 0.00456 (13404) covalent geometry : angle 0.56076 (18180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 2.322 Fit side-chains REVERT: E 451 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8596 (mt-10) outliers start: 4 outliers final: 0 residues processed: 191 average time/residue: 3.8873 time to fit residues: 790.4725 Evaluate side-chains 167 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 451 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135006 restraints weight = 33088.436| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.93 r_work: 0.3434 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13404 Z= 0.109 Angle : 0.478 3.520 18180 Z= 0.266 Chirality : 0.043 0.145 1920 Planarity : 0.004 0.027 2376 Dihedral : 4.301 20.024 1764 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.36 % Allowed : 13.75 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1584 helix: 0.64 (0.24), residues: 456 sheet: 3.05 (0.21), residues: 552 loop : -0.52 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 455 HIS 0.002 0.001 HIS E 468 PHE 0.014 0.002 PHE I 467 TYR 0.005 0.001 TYR H 398 ARG 0.002 0.000 ARG J 405 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 645) hydrogen bonds : angle 4.66208 ( 1755) covalent geometry : bond 0.00247 (13404) covalent geometry : angle 0.47830 (18180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: H 424 ASP cc_start: 0.7816 (p0) cc_final: 0.7547 (m-30) outliers start: 5 outliers final: 4 residues processed: 173 average time/residue: 4.0740 time to fit residues: 750.0403 Evaluate side-chains 171 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 121 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 GLN H 436 GLN K 436 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.168629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132573 restraints weight = 33587.250| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.95 r_work: 0.3404 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13404 Z= 0.140 Angle : 0.504 3.584 18180 Z= 0.281 Chirality : 0.044 0.148 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.364 20.282 1764 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.21 % Allowed : 13.60 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1584 helix: 0.57 (0.24), residues: 456 sheet: 3.00 (0.21), residues: 552 loop : -0.59 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.002 0.001 HIS B 468 PHE 0.014 0.002 PHE C 467 TYR 0.006 0.001 TYR B 398 ARG 0.002 0.000 ARG J 433 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 645) hydrogen bonds : angle 4.63761 ( 1755) covalent geometry : bond 0.00335 (13404) covalent geometry : angle 0.50382 (18180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8099 (ttm170) REVERT: E 433 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8014 (ttm170) REVERT: E 451 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: H 433 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8107 (ttm170) REVERT: K 433 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8102 (ttm170) outliers start: 17 outliers final: 4 residues processed: 181 average time/residue: 4.1775 time to fit residues: 800.4087 Evaluate side-chains 177 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN C 436 GLN F 436 GLN I 436 GLN L 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133626 restraints weight = 33402.633| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.92 r_work: 0.3401 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13404 Z= 0.130 Angle : 0.489 3.795 18180 Z= 0.273 Chirality : 0.044 0.147 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.314 19.803 1764 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.71 % Allowed : 13.68 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1584 helix: 0.61 (0.24), residues: 456 sheet: 3.02 (0.21), residues: 552 loop : -0.53 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 455 HIS 0.003 0.001 HIS K 468 PHE 0.014 0.002 PHE I 467 TYR 0.005 0.001 TYR E 398 ARG 0.002 0.000 ARG J 433 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 645) hydrogen bonds : angle 4.59921 ( 1755) covalent geometry : bond 0.00306 (13404) covalent geometry : angle 0.48921 (18180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8039 (ttm170) REVERT: B 451 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: C 451 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: E 433 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8025 (ttm170) REVERT: E 451 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: F 451 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: H 433 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8051 (ttm170) REVERT: H 451 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: I 451 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8455 (mt-10) REVERT: K 433 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8038 (ttm170) REVERT: K 451 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: L 451 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8447 (mt-10) outliers start: 24 outliers final: 4 residues processed: 180 average time/residue: 4.0833 time to fit residues: 779.8892 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 433 ARG Chi-restraints excluded: chain L residue 451 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 436 GLN G 436 GLN J 436 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.167009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131471 restraints weight = 33524.353| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.93 r_work: 0.3367 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13404 Z= 0.196 Angle : 0.548 4.030 18180 Z= 0.309 Chirality : 0.046 0.152 1920 Planarity : 0.005 0.029 2376 Dihedral : 4.519 19.911 1764 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.71 % Allowed : 13.68 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1584 helix: 0.34 (0.24), residues: 456 sheet: 2.88 (0.21), residues: 552 loop : -0.70 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 455 HIS 0.003 0.001 HIS E 468 PHE 0.013 0.002 PHE H 467 TYR 0.008 0.002 TYR H 398 ARG 0.003 0.000 ARG J 405 Details of bonding type rmsd hydrogen bonds : bond 0.05465 ( 645) hydrogen bonds : angle 4.75451 ( 1755) covalent geometry : bond 0.00477 (13404) covalent geometry : angle 0.54844 (18180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8064 (ttm170) REVERT: B 451 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: C 451 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: E 433 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8048 (ttm170) REVERT: E 451 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8622 (mt-10) REVERT: F 451 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: H 433 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8062 (ttm170) REVERT: H 451 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8700 (mt-10) REVERT: I 451 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: K 433 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8058 (ttm170) REVERT: K 451 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8685 (mt-10) REVERT: L 451 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8557 (mt-10) outliers start: 24 outliers final: 4 residues processed: 180 average time/residue: 3.8737 time to fit residues: 740.6668 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 433 ARG Chi-restraints excluded: chain L residue 451 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133080 restraints weight = 33534.293| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.93 r_work: 0.3399 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13404 Z= 0.123 Angle : 0.491 4.091 18180 Z= 0.274 Chirality : 0.044 0.144 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.372 19.662 1764 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.07 % Allowed : 14.81 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1584 helix: 0.49 (0.24), residues: 456 sheet: 2.98 (0.21), residues: 552 loop : -0.58 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.002 0.001 HIS H 468 PHE 0.014 0.002 PHE K 467 TYR 0.004 0.001 TYR B 398 ARG 0.002 0.000 ARG J 433 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 645) hydrogen bonds : angle 4.61595 ( 1755) covalent geometry : bond 0.00291 (13404) covalent geometry : angle 0.49060 (18180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8036 (ttm170) REVERT: B 451 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: C 451 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: E 433 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8016 (ttm170) REVERT: E 451 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: F 451 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: H 433 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8113 (ttm170) REVERT: I 451 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: K 433 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8093 (ttm170) REVERT: L 451 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8457 (mt-10) outliers start: 15 outliers final: 4 residues processed: 178 average time/residue: 4.0297 time to fit residues: 762.4744 Evaluate side-chains 178 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Chi-restraints excluded: chain L residue 451 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135689 restraints weight = 33244.824| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.92 r_work: 0.3433 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13404 Z= 0.100 Angle : 0.460 4.233 18180 Z= 0.254 Chirality : 0.043 0.144 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.202 19.693 1764 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.14 % Allowed : 14.53 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1584 helix: 0.69 (0.24), residues: 456 sheet: 3.00 (0.21), residues: 552 loop : -0.40 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 455 HIS 0.002 0.000 HIS D 395 PHE 0.015 0.002 PHE L 467 TYR 0.003 0.001 TYR I 398 ARG 0.003 0.000 ARG G 396 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 645) hydrogen bonds : angle 4.43518 ( 1755) covalent geometry : bond 0.00230 (13404) covalent geometry : angle 0.45994 (18180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8037 (ttm170) REVERT: B 451 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: C 451 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: E 433 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8011 (ttm170) REVERT: E 451 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: F 451 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8441 (mt-10) REVERT: H 433 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: H 451 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: I 451 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: K 433 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8039 (ttm170) REVERT: K 451 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8483 (mt-10) REVERT: L 451 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8424 (mt-10) outliers start: 16 outliers final: 4 residues processed: 181 average time/residue: 4.0775 time to fit residues: 783.4927 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 433 ARG Chi-restraints excluded: chain L residue 451 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.167043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131572 restraints weight = 33693.993| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.93 r_work: 0.3377 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13404 Z= 0.193 Angle : 0.543 4.316 18180 Z= 0.305 Chirality : 0.045 0.151 1920 Planarity : 0.005 0.028 2376 Dihedral : 4.446 19.875 1764 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.42 % Allowed : 14.53 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1584 helix: 0.44 (0.24), residues: 456 sheet: 2.63 (0.21), residues: 588 loop : -0.37 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 455 HIS 0.003 0.001 HIS D 468 PHE 0.013 0.002 PHE H 467 TYR 0.008 0.002 TYR E 398 ARG 0.003 0.000 ARG G 405 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 645) hydrogen bonds : angle 4.66285 ( 1755) covalent geometry : bond 0.00474 (13404) covalent geometry : angle 0.54302 (18180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8075 (ttm170) REVERT: B 451 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8670 (mt-10) REVERT: C 451 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: E 433 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: E 451 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8597 (mt-10) REVERT: F 451 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8556 (mt-10) REVERT: H 433 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8065 (ttm170) REVERT: H 451 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8696 (mt-10) REVERT: I 451 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8523 (mt-10) REVERT: K 433 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8060 (ttm170) REVERT: K 451 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: L 451 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8530 (mt-10) outliers start: 20 outliers final: 4 residues processed: 184 average time/residue: 3.9612 time to fit residues: 774.7211 Evaluate side-chains 176 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 433 ARG Chi-restraints excluded: chain L residue 451 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.0020 chunk 87 optimal weight: 0.6980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134167 restraints weight = 33335.463| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.93 r_work: 0.3418 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13404 Z= 0.108 Angle : 0.476 4.325 18180 Z= 0.264 Chirality : 0.043 0.143 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.276 19.617 1764 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.21 % Allowed : 14.74 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1584 helix: 0.61 (0.24), residues: 456 sheet: 2.74 (0.21), residues: 588 loop : -0.19 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.002 0.000 HIS A 395 PHE 0.014 0.002 PHE B 467 TYR 0.003 0.001 TYR I 398 ARG 0.002 0.000 ARG J 433 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 645) hydrogen bonds : angle 4.52450 ( 1755) covalent geometry : bond 0.00251 (13404) covalent geometry : angle 0.47583 (18180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8051 (ttm170) REVERT: B 451 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: C 451 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: E 433 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: E 451 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8485 (mt-10) REVERT: F 451 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: H 433 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8049 (ttm170) REVERT: H 451 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: I 451 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8441 (mt-10) REVERT: K 433 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8044 (ttm170) REVERT: K 451 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: L 451 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8461 (mt-10) outliers start: 17 outliers final: 4 residues processed: 180 average time/residue: 4.0958 time to fit residues: 785.6764 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 433 ARG Chi-restraints excluded: chain L residue 451 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 0.3980 chunk 129 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.169857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134736 restraints weight = 33322.900| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.92 r_work: 0.3416 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13404 Z= 0.117 Angle : 0.478 4.363 18180 Z= 0.264 Chirality : 0.044 0.145 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.233 19.723 1764 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.14 % Allowed : 14.96 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.21), residues: 1584 helix: 0.69 (0.24), residues: 456 sheet: 2.71 (0.21), residues: 588 loop : -0.13 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.002 0.001 HIS K 468 PHE 0.014 0.002 PHE F 467 TYR 0.005 0.001 TYR E 398 ARG 0.004 0.000 ARG B 396 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 645) hydrogen bonds : angle 4.46264 ( 1755) covalent geometry : bond 0.00278 (13404) covalent geometry : angle 0.47797 (18180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19695.92 seconds wall clock time: 337 minutes 17.17 seconds (20237.17 seconds total)