Starting phenix.real_space_refine on Sun Oct 12 15:43:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t15_40955/10_2025/8t15_40955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t15_40955/10_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_40955/10_2025/8t15_40955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t15_40955/10_2025/8t15_40955.map" model { file = "/net/cci-nas-00/data/ceres_data/8t15_40955/10_2025/8t15_40955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t15_40955/10_2025/8t15_40955.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.097 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.09, per 1000 atoms: 0.20 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: 2.54 Conformation dependent library (CDL) restraints added in 860.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.68 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: 5.70 Time building geometry restraints manager: 3.47 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (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 ARG 0.004 0.000 ARG G 396 TYR 0.005 0.001 TYR K 398 PHE 0.013 0.002 PHE K 467 TRP 0.006 0.001 TRP L 455 HIS 0.002 0.000 HIS H 420 Details of bonding type rmsd covalent geometry : bond 0.00248 (13404) covalent geometry : angle 0.53254 (18180) hydrogen bonds : bond 0.15570 ( 645) hydrogen bonds : angle 5.25980 ( 1755) *********************** 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 : 0.711 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: 2.2139 time to fit residues: 503.8853 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 : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.168083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131776 restraints weight = 33444.374| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.96 r_work: 0.3399 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13404 Z= 0.166 Angle : 0.538 3.824 18180 Z= 0.303 Chirality : 0.045 0.154 1920 Planarity : 0.005 0.027 2376 Dihedral : 4.480 21.420 1764 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.07 % Allowed : 12.54 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1584 helix: 0.52 (0.24), residues: 456 sheet: 3.03 (0.21), residues: 552 loop : -0.62 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 405 TYR 0.009 0.002 TYR B 398 PHE 0.013 0.002 PHE H 467 TRP 0.006 0.001 TRP I 455 HIS 0.003 0.001 HIS H 468 Details of bonding type rmsd covalent geometry : bond 0.00391 (13404) covalent geometry : angle 0.53776 (18180) hydrogen bonds : bond 0.05450 ( 645) hydrogen bonds : angle 4.89274 ( 1755) *********************** 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 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.679 Fit side-chains REVERT: E 451 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8595 (mt-10) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 2.0963 time to fit residues: 399.7420 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 : 0.750 ------------------------------------------------------------------------------- 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 60 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 GLN E 436 GLN H 436 GLN K 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132532 restraints weight = 33483.634| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.95 r_work: 0.3399 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0884 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= 0.158 Angle : 0.521 3.595 18180 Z= 0.293 Chirality : 0.045 0.149 1920 Planarity : 0.004 0.027 2376 Dihedral : 4.459 20.229 1764 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.85 % Allowed : 12.82 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1584 helix: 0.48 (0.24), residues: 456 sheet: 2.95 (0.21), residues: 552 loop : -0.66 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 433 TYR 0.007 0.001 TYR H 398 PHE 0.014 0.002 PHE H 467 TRP 0.006 0.001 TRP I 455 HIS 0.002 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00372 (13404) covalent geometry : angle 0.52101 (18180) hydrogen bonds : bond 0.05285 ( 645) hydrogen bonds : angle 4.77841 ( 1755) *********************** 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 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7993 (ttm170) REVERT: B 451 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: E 433 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8035 (ttm170) REVERT: E 451 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: H 433 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7980 (ttm170) REVERT: H 451 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: K 433 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7979 (ttm170) REVERT: K 451 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8600 (mt-10) outliers start: 12 outliers final: 4 residues processed: 180 average time/residue: 2.2030 time to fit residues: 418.7327 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU 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 12 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 0.0170 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.168059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132442 restraints weight = 33400.645| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.93 r_work: 0.3408 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1027 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= 0.153 Angle : 0.513 3.633 18180 Z= 0.288 Chirality : 0.045 0.148 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.458 20.223 1764 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.28 % Allowed : 12.25 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.21), residues: 1584 helix: 0.41 (0.24), residues: 456 sheet: 2.93 (0.21), residues: 552 loop : -0.68 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 433 TYR 0.006 0.001 TYR E 398 PHE 0.014 0.002 PHE H 467 TRP 0.005 0.001 TRP A 455 HIS 0.002 0.001 HIS E 468 Details of bonding type rmsd covalent geometry : bond 0.00367 (13404) covalent geometry : angle 0.51344 (18180) hydrogen bonds : bond 0.04956 ( 645) hydrogen bonds : angle 4.72796 ( 1755) *********************** 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 200 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8012 (ttm170) REVERT: B 451 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: C 451 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: E 433 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8011 (ttm170) REVERT: E 451 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: F 451 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: H 433 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: H 451 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: I 451 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: K 433 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: K 451 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: L 451 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8504 (mt-10) outliers start: 32 outliers final: 4 residues processed: 188 average time/residue: 2.2182 time to fit residues: 440.2276 Evaluate side-chains 188 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 6 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.170251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135223 restraints weight = 33425.068| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.92 r_work: 0.3417 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1082 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= 0.118 Angle : 0.478 3.781 18180 Z= 0.266 Chirality : 0.044 0.146 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.314 19.869 1764 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.64 % Allowed : 13.18 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.21), residues: 1584 helix: 0.57 (0.23), residues: 456 sheet: 3.03 (0.21), residues: 552 loop : -0.58 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 433 TYR 0.005 0.001 TYR K 398 PHE 0.014 0.002 PHE C 467 TRP 0.005 0.001 TRP F 455 HIS 0.002 0.001 HIS K 468 Details of bonding type rmsd covalent geometry : bond 0.00275 (13404) covalent geometry : angle 0.47787 (18180) hydrogen bonds : bond 0.04313 ( 645) hydrogen bonds : angle 4.57304 ( 1755) *********************** 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 184 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.752 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: 0.8024 (ttm170) REVERT: B 451 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: E 433 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8016 (ttm170) REVERT: E 451 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: H 433 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8033 (ttm170) REVERT: H 451 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: K 433 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8021 (ttm170) REVERT: K 451 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8527 (mt-10) outliers start: 23 outliers final: 4 residues processed: 175 average time/residue: 1.9713 time to fit residues: 365.5715 Evaluate side-chains 173 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.168062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132727 restraints weight = 33559.708| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.93 r_work: 0.3396 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13404 Z= 0.151 Angle : 0.506 3.994 18180 Z= 0.284 Chirality : 0.044 0.148 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.395 19.924 1764 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.07 % Allowed : 13.75 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.21), residues: 1584 helix: 0.47 (0.24), residues: 456 sheet: 2.94 (0.21), residues: 552 loop : -0.63 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 405 TYR 0.006 0.001 TYR B 398 PHE 0.014 0.002 PHE C 467 TRP 0.005 0.001 TRP I 455 HIS 0.003 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00362 (13404) covalent geometry : angle 0.50629 (18180) hydrogen bonds : bond 0.04806 ( 645) hydrogen bonds : angle 4.64764 ( 1755) *********************** 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 179 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8036 (ttm170) REVERT: B 451 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: E 433 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: E 451 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: H 433 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: H 451 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: I 451 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8499 (mt-10) REVERT: J 451 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: K 433 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: K 451 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8588 (mt-10) REVERT: L 451 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8499 (mt-10) outliers start: 15 outliers final: 4 residues processed: 179 average time/residue: 2.1688 time to fit residues: 410.6331 Evaluate side-chains 179 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J 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 31 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.169871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134779 restraints weight = 33369.664| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.92 r_work: 0.3440 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1185 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= 0.109 Angle : 0.468 4.113 18180 Z= 0.260 Chirality : 0.043 0.144 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.246 19.587 1764 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.14 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.21), residues: 1584 helix: 0.65 (0.24), residues: 456 sheet: 3.03 (0.21), residues: 552 loop : -0.48 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 396 TYR 0.002 0.001 TYR H 369 PHE 0.014 0.002 PHE C 467 TRP 0.005 0.001 TRP F 455 HIS 0.002 0.001 HIS E 468 Details of bonding type rmsd covalent geometry : bond 0.00253 (13404) covalent geometry : angle 0.46839 (18180) hydrogen bonds : bond 0.04076 ( 645) hydrogen bonds : angle 4.50036 ( 1755) *********************** 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 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8030 (ttm170) REVERT: B 451 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: E 433 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8013 (ttm170) REVERT: E 451 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: H 433 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8022 (ttm170) REVERT: H 451 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: I 451 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: K 433 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7994 (ttm170) REVERT: K 451 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: L 451 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8459 (mt-10) outliers start: 16 outliers final: 4 residues processed: 180 average time/residue: 2.1500 time to fit residues: 409.3724 Evaluate side-chains 178 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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 78 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134183 restraints weight = 33465.969| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.84 r_work: 0.3398 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1217 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= 0.133 Angle : 0.488 4.237 18180 Z= 0.272 Chirality : 0.044 0.146 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.295 19.727 1764 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.07 % Allowed : 13.96 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1584 helix: 0.61 (0.24), residues: 456 sheet: 2.96 (0.21), residues: 552 loop : -0.50 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 405 TYR 0.005 0.001 TYR E 398 PHE 0.014 0.002 PHE C 467 TRP 0.005 0.001 TRP F 455 HIS 0.002 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00318 (13404) covalent geometry : angle 0.48812 (18180) hydrogen bonds : bond 0.04422 ( 645) hydrogen bonds : angle 4.54022 ( 1755) *********************** 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 179 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7965 (ttm170) REVERT: B 451 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: E 433 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7954 (ttm170) REVERT: E 451 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8523 (mt-10) REVERT: H 433 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7959 (ttm170) REVERT: H 451 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: I 451 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: J 451 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: K 433 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7951 (ttm170) REVERT: K 451 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8547 (mt-10) REVERT: L 451 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8463 (mt-10) outliers start: 15 outliers final: 4 residues processed: 179 average time/residue: 2.1753 time to fit residues: 411.9164 Evaluate side-chains 179 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 H residue 451 GLU Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J 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 29 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135874 restraints weight = 33440.265| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.93 r_work: 0.3446 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13404 Z= 0.100 Angle : 0.457 4.007 18180 Z= 0.252 Chirality : 0.043 0.142 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.161 19.462 1764 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 13.75 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.21), residues: 1584 helix: 0.79 (0.24), residues: 456 sheet: 2.75 (0.22), residues: 588 loop : -0.10 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 405 TYR 0.003 0.001 TYR A 398 PHE 0.014 0.002 PHE C 467 TRP 0.005 0.001 TRP I 455 HIS 0.001 0.000 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00231 (13404) covalent geometry : angle 0.45732 (18180) hydrogen bonds : bond 0.03805 ( 645) hydrogen bonds : angle 4.40481 ( 1755) *********************** 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 197 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8015 (ttm170) REVERT: B 451 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: E 424 ASP cc_start: 0.7808 (p0) cc_final: 0.7447 (m-30) REVERT: E 433 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8009 (ttm170) REVERT: E 451 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: H 433 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7999 (ttm170) REVERT: H 451 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: I 451 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: K 433 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: K 451 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: L 451 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8443 (mt-10) outliers start: 18 outliers final: 4 residues processed: 187 average time/residue: 2.1055 time to fit residues: 416.5282 Evaluate side-chains 189 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 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 45 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134536 restraints weight = 33512.196| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.87 r_work: 0.3402 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13404 Z= 0.151 Angle : 0.504 4.048 18180 Z= 0.281 Chirality : 0.044 0.147 1920 Planarity : 0.004 0.029 2376 Dihedral : 4.294 19.631 1764 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.00 % Allowed : 14.25 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.21), residues: 1584 helix: 0.62 (0.24), residues: 456 sheet: 2.70 (0.21), residues: 588 loop : -0.24 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 405 TYR 0.007 0.001 TYR K 398 PHE 0.014 0.002 PHE C 467 TRP 0.005 0.001 TRP F 455 HIS 0.003 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00365 (13404) covalent geometry : angle 0.50361 (18180) hydrogen bonds : bond 0.04601 ( 645) hydrogen bonds : angle 4.55528 ( 1755) ********************** 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 178 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: B 451 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: E 433 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7952 (ttm170) REVERT: E 451 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8559 (mt-10) REVERT: H 433 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7967 (ttm170) REVERT: H 451 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: I 451 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: K 433 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7959 (ttm170) REVERT: K 451 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8584 (mt-10) REVERT: L 451 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8505 (mt-10) outliers start: 14 outliers final: 4 residues processed: 178 average time/residue: 1.9542 time to fit residues: 368.3799 Evaluate side-chains 178 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 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 145 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.170815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135921 restraints weight = 33257.459| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.92 r_work: 0.3458 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1259 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= 0.106 Angle : 0.465 4.021 18180 Z= 0.257 Chirality : 0.043 0.142 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.177 19.450 1764 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 13.82 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.21), residues: 1584 helix: 0.80 (0.24), residues: 456 sheet: 2.74 (0.22), residues: 588 loop : -0.11 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 396 TYR 0.003 0.001 TYR L 398 PHE 0.014 0.002 PHE F 467 TRP 0.005 0.001 TRP I 455 HIS 0.001 0.000 HIS J 395 Details of bonding type rmsd covalent geometry : bond 0.00247 (13404) covalent geometry : angle 0.46498 (18180) hydrogen bonds : bond 0.03935 ( 645) hydrogen bonds : angle 4.43191 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10424.53 seconds wall clock time: 177 minutes 1.32 seconds (10621.32 seconds total)