Starting phenix.real_space_refine on Sun Jun 22 02:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t15_40955/06_2025/8t15_40955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t15_40955/06_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_40955/06_2025/8t15_40955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t15_40955/06_2025/8t15_40955.map" model { file = "/net/cci-nas-00/data/ceres_data/8t15_40955/06_2025/8t15_40955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t15_40955/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.34, per 1000 atoms: 0.52 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: 6.57 Conformation dependent library (CDL) restraints added in 2.2 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: 2.11 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: 8.97 Time building geometry restraints manager: 7.95 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: 5.190 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: 0.410 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.630 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.440 ------------------------------------------------------------------------------- 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 : 2.109 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: 4.2794 time to fit residues: 978.2217 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 : 2.240 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132431 restraints weight = 33430.554| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 1.943 Fit side-chains REVERT: E 451 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8603 (mt-10) outliers start: 4 outliers final: 0 residues processed: 191 average time/residue: 3.8642 time to fit residues: 785.2747 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 : 2.033 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.3943 r_free = 0.3943 target = 0.170727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135117 restraints weight = 33104.846| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.93 r_work: 0.3438 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13404 Z= 0.111 Angle : 0.477 3.468 18180 Z= 0.265 Chirality : 0.043 0.145 1920 Planarity : 0.004 0.027 2376 Dihedral : 4.292 20.010 1764 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.36 % Allowed : 13.68 % Favored : 85.97 % 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: 1.68 (0.21), residues: 1584 helix: 0.65 (0.24), residues: 456 sheet: 3.04 (0.21), residues: 552 loop : -0.52 (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 E 468 PHE 0.014 0.002 PHE I 467 TYR 0.005 0.001 TYR B 398 ARG 0.002 0.000 ARG J 433 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 645) hydrogen bonds : angle 4.64462 ( 1755) covalent geometry : bond 0.00253 (13404) covalent geometry : angle 0.47658 (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 178 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: H 424 ASP cc_start: 0.7810 (p0) cc_final: 0.7547 (m-30) outliers start: 5 outliers final: 4 residues processed: 178 average time/residue: 4.2069 time to fit residues: 796.3394 Evaluate side-chains 175 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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: 0.8980 chunk 116 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136766 restraints weight = 33504.836| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.80 r_work: 0.3415 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0994 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= 0.125 Angle : 0.486 3.568 18180 Z= 0.270 Chirality : 0.044 0.146 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.278 19.994 1764 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.21 % Allowed : 13.53 % Favored : 85.26 % 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: 1.69 (0.21), residues: 1584 helix: 0.66 (0.24), residues: 456 sheet: 3.04 (0.21), residues: 552 loop : -0.48 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 455 HIS 0.002 0.001 HIS B 468 PHE 0.015 0.002 PHE L 467 TYR 0.005 0.001 TYR B 398 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 645) hydrogen bonds : angle 4.55205 ( 1755) covalent geometry : bond 0.00296 (13404) covalent geometry : angle 0.48588 (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 187 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8029 (ttm170) REVERT: E 433 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7938 (ttm170) REVERT: E 451 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: H 424 ASP cc_start: 0.7769 (p0) cc_final: 0.7470 (m-30) REVERT: H 433 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8033 (ttm170) REVERT: K 433 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8023 (ttm170) outliers start: 17 outliers final: 4 residues processed: 182 average time/residue: 4.2072 time to fit residues: 811.0788 Evaluate side-chains 174 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 436 GLN F 436 GLN I 436 GLN L 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134506 restraints weight = 33400.919| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.93 r_work: 0.3414 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13404 Z= 0.117 Angle : 0.476 3.866 18180 Z= 0.264 Chirality : 0.044 0.146 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.229 19.642 1764 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.78 % Allowed : 13.60 % 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: 1.78 (0.21), residues: 1584 helix: 0.72 (0.24), residues: 456 sheet: 3.09 (0.21), residues: 552 loop : -0.41 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 455 HIS 0.002 0.001 HIS E 468 PHE 0.014 0.002 PHE C 467 TYR 0.005 0.001 TYR B 398 ARG 0.002 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 645) hydrogen bonds : angle 4.51753 ( 1755) covalent geometry : bond 0.00273 (13404) covalent geometry : angle 0.47564 (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 192 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8045 (ttm170) REVERT: B 451 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: C 451 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: E 433 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8009 (ttm170) REVERT: E 451 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: F 451 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: H 424 ASP cc_start: 0.7804 (p0) cc_final: 0.7489 (m-30) REVERT: H 433 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8060 (ttm170) REVERT: H 451 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: I 451 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8456 (mt-10) REVERT: K 433 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8056 (ttm170) REVERT: K 451 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: L 451 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8429 (mt-10) outliers start: 25 outliers final: 4 residues processed: 184 average time/residue: 4.1870 time to fit residues: 816.7036 Evaluate side-chains 181 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN D 436 GLN G 436 GLN J 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131113 restraints weight = 33464.750| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.98 r_work: 0.3373 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13404 Z= 0.163 Angle : 0.523 3.971 18180 Z= 0.293 Chirality : 0.045 0.148 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.399 19.800 1764 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.64 % Allowed : 13.75 % 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: 1.56 (0.21), residues: 1584 helix: 0.51 (0.24), residues: 456 sheet: 2.98 (0.21), residues: 552 loop : -0.54 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.004 0.001 HIS K 468 PHE 0.014 0.002 PHE E 467 TYR 0.007 0.001 TYR B 398 ARG 0.003 0.000 ARG G 405 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 645) hydrogen bonds : angle 4.65946 ( 1755) covalent geometry : bond 0.00392 (13404) covalent geometry : angle 0.52282 (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: 23 poor density : 165 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8037 (ttm170) REVERT: B 451 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8671 (mt-10) REVERT: C 451 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: E 433 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8013 (ttm170) REVERT: E 451 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: F 451 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: H 433 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: H 451 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8690 (mt-10) REVERT: I 451 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8526 (mt-10) REVERT: K 433 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: K 451 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: L 451 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8528 (mt-10) outliers start: 23 outliers final: 4 residues processed: 181 average time/residue: 5.3174 time to fit residues: 1032.4113 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 : 2.487 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 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 = 0.168805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133190 restraints weight = 33582.162| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.94 r_work: 0.3420 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1178 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= 0.121 Angle : 0.483 4.095 18180 Z= 0.269 Chirality : 0.044 0.145 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.290 19.634 1764 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % 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: 1.69 (0.21), residues: 1584 helix: 0.63 (0.24), residues: 456 sheet: 3.02 (0.21), residues: 552 loop : -0.45 (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 E 467 TYR 0.003 0.001 TYR D 369 ARG 0.002 0.000 ARG J 433 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 645) hydrogen bonds : angle 4.54460 ( 1755) covalent geometry : bond 0.00286 (13404) covalent geometry : angle 0.48279 (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 182 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8037 (ttm170) REVERT: B 451 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: C 451 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: E 433 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: E 451 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: F 451 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8492 (mt-10) REVERT: H 433 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8046 (ttm170) REVERT: H 451 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8605 (mt-10) REVERT: I 451 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: K 433 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8033 (ttm170) REVERT: K 451 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8601 (mt-10) REVERT: L 451 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8472 (mt-10) outliers start: 18 outliers final: 4 residues processed: 180 average time/residue: 4.1044 time to fit residues: 784.8589 Evaluate side-chains 179 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.169309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133216 restraints weight = 33278.232| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.98 r_work: 0.3434 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1211 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= 0.119 Angle : 0.477 4.314 18180 Z= 0.264 Chirality : 0.044 0.145 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.228 19.657 1764 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.21 % Allowed : 14.17 % 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: 1.72 (0.21), residues: 1584 helix: 0.66 (0.24), residues: 456 sheet: 3.02 (0.21), residues: 552 loop : -0.41 (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 K 468 PHE 0.014 0.002 PHE F 467 TYR 0.004 0.001 TYR H 398 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 645) hydrogen bonds : angle 4.48067 ( 1755) covalent geometry : bond 0.00282 (13404) covalent geometry : angle 0.47687 (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: 17 poor density : 169 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7976 (ttm170) REVERT: B 451 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: C 451 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: E 433 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7988 (ttm170) REVERT: E 451 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: F 451 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: H 433 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8017 (ttm170) REVERT: H 451 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8585 (mt-10) REVERT: I 451 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8455 (mt-10) REVERT: K 433 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8011 (ttm170) REVERT: K 451 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: L 451 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8475 (mt-10) outliers start: 17 outliers final: 4 residues processed: 185 average time/residue: 4.8605 time to fit residues: 957.7439 Evaluate side-chains 181 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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: 0.7980 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: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.166676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130241 restraints weight = 33691.254| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.98 r_work: 0.3392 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13404 Z= 0.186 Angle : 0.538 4.320 18180 Z= 0.301 Chirality : 0.045 0.150 1920 Planarity : 0.005 0.029 2376 Dihedral : 4.423 19.583 1764 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.14 % Allowed : 14.81 % 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: 1.51 (0.21), residues: 1584 helix: 0.44 (0.24), residues: 456 sheet: 2.61 (0.21), residues: 588 loop : -0.36 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.003 0.001 HIS J 468 PHE 0.013 0.002 PHE K 467 TYR 0.006 0.002 TYR A 369 ARG 0.003 0.000 ARG G 405 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 645) hydrogen bonds : angle 4.66261 ( 1755) covalent geometry : bond 0.00458 (13404) covalent geometry : angle 0.53763 (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 183 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8052 (ttm170) REVERT: B 451 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8681 (mt-10) REVERT: C 451 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: E 433 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: E 451 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8614 (mt-10) REVERT: F 451 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: H 433 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8040 (ttm170) REVERT: H 451 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8709 (mt-10) REVERT: I 451 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: K 433 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8028 (ttm170) REVERT: K 451 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8687 (mt-10) REVERT: L 451 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8541 (mt-10) outliers start: 16 outliers final: 4 residues processed: 183 average time/residue: 4.4623 time to fit residues: 873.1654 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 : 2.109 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 46 optimal weight: 0.0980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.171451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136409 restraints weight = 33246.782| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.93 r_work: 0.3447 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1275 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= 0.093 Angle : 0.457 4.326 18180 Z= 0.252 Chirality : 0.043 0.140 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.149 19.215 1764 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.14 % Allowed : 14.81 % 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: 1.93 (0.21), residues: 1584 helix: 0.79 (0.24), residues: 456 sheet: 2.80 (0.22), residues: 588 loop : -0.03 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 455 HIS 0.002 0.001 HIS F 395 PHE 0.014 0.002 PHE F 467 TYR 0.004 0.000 TYR J 398 ARG 0.004 0.000 ARG E 396 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 645) hydrogen bonds : angle 4.40074 ( 1755) covalent geometry : bond 0.00212 (13404) covalent geometry : angle 0.45727 (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 189 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 TYR cc_start: 0.7311 (m-80) cc_final: 0.7090 (m-80) REVERT: B 433 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8061 (ttm170) REVERT: D 398 TYR cc_start: 0.7329 (m-80) cc_final: 0.7093 (m-80) REVERT: E 433 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: E 451 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: F 398 TYR cc_start: 0.7422 (m-80) cc_final: 0.7173 (m-80) REVERT: G 398 TYR cc_start: 0.7321 (m-80) cc_final: 0.7103 (m-80) REVERT: H 433 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8053 (ttm170) REVERT: J 398 TYR cc_start: 0.7319 (m-80) cc_final: 0.7078 (m-80) REVERT: K 433 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8060 (ttm170) outliers start: 16 outliers final: 4 residues processed: 178 average time/residue: 4.2092 time to fit residues: 803.3711 Evaluate side-chains 182 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 2.284 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.171601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136642 restraints weight = 33283.004| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.93 r_work: 0.3436 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13404 Z= 0.103 Angle : 0.463 4.069 18180 Z= 0.253 Chirality : 0.043 0.144 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.105 19.433 1764 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.85 % Allowed : 14.89 % Favored : 84.26 % 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: 1.98 (0.21), residues: 1584 helix: 0.85 (0.24), residues: 456 sheet: 2.79 (0.22), residues: 588 loop : 0.01 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 455 HIS 0.002 0.000 HIS L 468 PHE 0.015 0.002 PHE F 467 TYR 0.004 0.001 TYR K 398 ARG 0.002 0.000 ARG H 396 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 645) hydrogen bonds : angle 4.34677 ( 1755) covalent geometry : bond 0.00244 (13404) covalent geometry : angle 0.46313 (18180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21262.66 seconds wall clock time: 369 minutes 35.37 seconds (22175.37 seconds total)