Starting phenix.real_space_refine on Sat Jul 4 09:59:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.map" model { file = "/net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xer_33158/07_2026/7xer_33158.cif" } resolution = 2.47 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13168 2.51 5 N 3368 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20084 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.80, per 1000 atoms: 0.19 Number of scatterers: 20084 At special positions: 0 Unit cell: (156.156, 155.142, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3440 8.00 N 3368 7.00 C 13168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 819.1 milliseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 63.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.547A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.767A pdb=" N LEU A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.960A pdb=" N ARG A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.549A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.733A pdb=" N LEU A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.708A pdb=" N ARG A 366 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 367 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 384 Processing helix chain 'A' and resid 384 through 408 Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 467 through 488 removed outlier: 3.807A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 511 removed outlier: 3.825A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 531 Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.630A pdb=" N GLY A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.566A pdb=" N THR A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 647 through 668 removed outlier: 4.046A pdb=" N TRP A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.736A pdb=" N TRP A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.547A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.768A pdb=" N LEU B 134 " --> pdb=" O CYS B 130 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.960A pdb=" N ARG B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.549A pdb=" N ILE B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.732A pdb=" N LEU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.708A pdb=" N ARG B 366 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 367 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 369 " --> pdb=" O ARG B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 384 through 408 Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 467 through 488 removed outlier: 3.806A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 511 removed outlier: 3.825A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.630A pdb=" N GLY B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 600 removed outlier: 3.566A pdb=" N THR B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 631 through 647 Processing helix chain 'B' and resid 647 through 668 removed outlier: 4.047A pdb=" N TRP B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.736A pdb=" N TRP B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.546A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.767A pdb=" N LEU C 134 " --> pdb=" O CYS C 130 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.960A pdb=" N ARG C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.549A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.733A pdb=" N LEU C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.708A pdb=" N ARG C 366 " --> pdb=" O HIS C 363 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 367 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 369 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 384 Processing helix chain 'C' and resid 384 through 408 Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 467 through 488 removed outlier: 3.807A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 511 removed outlier: 3.825A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP C 504 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 531 Processing helix chain 'C' and resid 532 through 553 removed outlier: 3.630A pdb=" N GLY C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 600 removed outlier: 3.565A pdb=" N THR C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 647 through 668 removed outlier: 4.046A pdb=" N TRP C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.736A pdb=" N TRP C 710 " --> pdb=" O ASN C 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.546A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.767A pdb=" N LEU D 134 " --> pdb=" O CYS D 130 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.960A pdb=" N ARG D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.550A pdb=" N ILE D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.732A pdb=" N LEU D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.708A pdb=" N ARG D 366 " --> pdb=" O HIS D 363 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 367 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 369 " --> pdb=" O ARG D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 384 Processing helix chain 'D' and resid 384 through 408 Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 467 through 488 removed outlier: 3.807A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 511 removed outlier: 3.825A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP D 504 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 505 " --> pdb=" O VAL D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 531 Processing helix chain 'D' and resid 532 through 553 removed outlier: 3.630A pdb=" N GLY D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 600 removed outlier: 3.565A pdb=" N THR D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 631 through 647 Processing helix chain 'D' and resid 647 through 668 removed outlier: 4.047A pdb=" N TRP D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.736A pdb=" N TRP D 710 " --> pdb=" O ASN D 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 684 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 684 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 684 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 684 " --> pdb=" O ARG D 697 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3156 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: 3.09 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6248 1.34 - 1.46: 4711 1.46 - 1.58: 9481 1.58 - 1.70: 0 1.70 - 1.81: 160 Bond restraints: 20600 Sorted by residual: bond pdb=" CA GLN C 311 " pdb=" CB GLN C 311 " ideal model delta sigma weight residual 1.526 1.578 -0.051 1.70e-02 3.46e+03 9.17e+00 bond pdb=" CA GLN D 311 " pdb=" CB GLN D 311 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.70e-02 3.46e+03 9.07e+00 bond pdb=" CA GLN A 311 " pdb=" CB GLN A 311 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.70e-02 3.46e+03 9.07e+00 bond pdb=" CA GLN B 311 " pdb=" CB GLN B 311 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.70e-02 3.46e+03 9.07e+00 bond pdb=" C GLN A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.335 1.360 -0.026 1.28e-02 6.10e+03 4.00e+00 ... (remaining 20595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 27372 2.18 - 4.35: 537 4.35 - 6.53: 51 6.53 - 8.71: 16 8.71 - 10.88: 4 Bond angle restraints: 27980 Sorted by residual: angle pdb=" N LEU D 532 " pdb=" CA LEU D 532 " pdb=" C LEU D 532 " ideal model delta sigma weight residual 114.62 107.98 6.64 1.14e+00 7.69e-01 3.39e+01 angle pdb=" N LEU B 532 " pdb=" CA LEU B 532 " pdb=" C LEU B 532 " ideal model delta sigma weight residual 114.62 107.99 6.63 1.14e+00 7.69e-01 3.38e+01 angle pdb=" N LEU A 532 " pdb=" CA LEU A 532 " pdb=" C LEU A 532 " ideal model delta sigma weight residual 114.62 108.02 6.60 1.14e+00 7.69e-01 3.35e+01 angle pdb=" N LEU C 532 " pdb=" CA LEU C 532 " pdb=" C LEU C 532 " ideal model delta sigma weight residual 114.62 108.05 6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" N VAL D 343 " pdb=" CA VAL D 343 " pdb=" C VAL D 343 " ideal model delta sigma weight residual 113.71 108.70 5.01 9.50e-01 1.11e+00 2.78e+01 ... (remaining 27975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 10882 16.47 - 32.95: 965 32.95 - 49.42: 156 49.42 - 65.89: 25 65.89 - 82.37: 24 Dihedral angle restraints: 12052 sinusoidal: 4884 harmonic: 7168 Sorted by residual: dihedral pdb=" CA ASP B 531 " pdb=" C ASP B 531 " pdb=" N LEU B 532 " pdb=" CA LEU B 532 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP C 531 " pdb=" C ASP C 531 " pdb=" N LEU C 532 " pdb=" CA LEU C 532 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP A 531 " pdb=" C ASP A 531 " pdb=" N LEU A 532 " pdb=" CA LEU A 532 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 12049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2696 0.057 - 0.113: 448 0.113 - 0.170: 20 0.170 - 0.227: 0 0.227 - 0.283: 12 Chirality restraints: 3176 Sorted by residual: chirality pdb=" C13 CLR D1001 " pdb=" C12 CLR D1001 " pdb=" C14 CLR D1001 " pdb=" C17 CLR D1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C13 CLR C1001 " pdb=" C12 CLR C1001 " pdb=" C14 CLR C1001 " pdb=" C17 CLR C1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C13 CLR B1001 " pdb=" C12 CLR B1001 " pdb=" C14 CLR B1001 " pdb=" C17 CLR B1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3173 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 693 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO D 694 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 694 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 694 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 693 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 694 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 693 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO C 694 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 694 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 694 " 0.029 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2565 2.76 - 3.29: 20218 3.29 - 3.83: 33545 3.83 - 4.36: 37808 4.36 - 4.90: 65798 Nonbonded interactions: 159934 Sorted by model distance: nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 464 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 461 " pdb=" OD1 ASP B 464 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 461 " pdb=" OD1 ASP A 464 " model vdw 2.220 3.040 nonbonded pdb=" OG SER D 461 " pdb=" OD1 ASP D 464 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR D 266 " pdb=" OE1 GLU D 283 " model vdw 2.281 3.040 ... (remaining 159929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.490 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.003 0.051 20600 Z= 0.174 Angle : 0.743 10.883 27980 Z= 0.436 Chirality : 0.042 0.283 3176 Planarity : 0.004 0.051 3428 Dihedral : 13.011 82.366 7428 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 0.23 % Allowed : 0.64 % Favored : 99.13 % 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 are not related in a simple way. whole: -0.04 (0.17), residues: 2432 helix: 1.51 (0.14), residues: 1444 sheet: -0.93 (0.51), residues: 84 loop : -2.64 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 512 TYR 0.023 0.002 TYR D 157 PHE 0.019 0.001 PHE A 467 TRP 0.015 0.001 TRP B 218 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (20600) covalent geometry : angle 0.74295 / 0.44 (27980) hydrogen bonds : bond 0.15700 / 10.45 ( 1068) hydrogen bonds : angle 5.03522 / 3.62 ( 3156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 342 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 685 LYS cc_start: 0.8555 (tttp) cc_final: 0.8352 (tptt) REVERT: C 272 MET cc_start: 0.7760 (tpp) cc_final: 0.7493 (tpp) outliers start: 5 outliers final: 0 residues processed: 347 average time/residue: 0.5761 time to fit residues: 225.5670 Evaluate side-chains 212 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 217 GLN A 258 ASN B 160 HIS B 217 GLN B 258 ASN C 160 HIS C 217 GLN C 258 ASN D 160 HIS D 217 GLN D 258 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.137779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093126 restraints weight = 35063.479| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.84 r_work: 0.3207 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20600 Z= 0.154 Angle : 0.615 5.574 27980 Z= 0.312 Chirality : 0.039 0.153 3176 Planarity : 0.004 0.051 3428 Dihedral : 4.839 43.033 2732 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.94 % Allowed : 10.29 % Favored : 86.76 % 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 are not related in a simple way. whole: 0.27 (0.17), residues: 2432 helix: 1.70 (0.14), residues: 1468 sheet: -0.51 (0.51), residues: 84 loop : -2.56 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 158 TYR 0.013 0.002 TYR C 223 PHE 0.023 0.001 PHE B 486 TRP 0.013 0.001 TRP B 218 HIS 0.005 0.001 HIS D 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (20600) covalent geometry : angle 0.61542 / 0.31 (27980) hydrogen bonds : bond 0.05049 / 3.39 ( 1068) hydrogen bonds : angle 4.08613 / 2.91 ( 3156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 234 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.6886 (tpm170) cc_final: 0.6684 (tpp-160) REVERT: A 609 GLU cc_start: 0.8554 (tp30) cc_final: 0.8041 (mm-30) REVERT: A 685 LYS cc_start: 0.8562 (tttp) cc_final: 0.8244 (tptt) REVERT: B 192 ARG cc_start: 0.6919 (tpm170) cc_final: 0.6693 (tpp-160) REVERT: B 609 GLU cc_start: 0.8535 (tp30) cc_final: 0.8003 (mm-30) REVERT: C 192 ARG cc_start: 0.6630 (tpm170) cc_final: 0.6238 (tpp-160) REVERT: C 321 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8394 (pp) REVERT: C 609 GLU cc_start: 0.8557 (tp30) cc_final: 0.8033 (mm-30) REVERT: D 434 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 602 MET cc_start: 0.9447 (mmm) cc_final: 0.9211 (mmp) REVERT: D 609 GLU cc_start: 0.8535 (tp30) cc_final: 0.8013 (mm-30) outliers start: 64 outliers final: 10 residues processed: 265 average time/residue: 0.5448 time to fit residues: 166.9107 Evaluate side-chains 215 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 435 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 0.9990 chunk 120 optimal weight: 0.0770 chunk 148 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.139242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094943 restraints weight = 35213.839| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.57 r_work: 0.3254 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20600 Z= 0.115 Angle : 0.532 5.175 27980 Z= 0.271 Chirality : 0.037 0.158 3176 Planarity : 0.003 0.049 3428 Dihedral : 4.523 44.066 2732 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.34 % Allowed : 14.43 % Favored : 83.23 % 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 are not related in a simple way. whole: 0.56 (0.17), residues: 2432 helix: 1.95 (0.14), residues: 1464 sheet: -0.20 (0.51), residues: 84 loop : -2.46 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 158 TYR 0.017 0.001 TYR B 466 PHE 0.013 0.001 PHE C 467 TRP 0.010 0.001 TRP C 218 HIS 0.004 0.001 HIS D 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (20600) covalent geometry : angle 0.53192 / 0.27 (27980) hydrogen bonds : bond 0.04158 / 2.80 ( 1068) hydrogen bonds : angle 3.80126 / 2.69 ( 3156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.745 Fit side-chains REVERT: A 192 ARG cc_start: 0.6906 (tpm170) cc_final: 0.6607 (tpp-160) REVERT: A 463 MET cc_start: 0.8188 (tpt) cc_final: 0.7978 (tpp) REVERT: A 609 GLU cc_start: 0.8576 (tp30) cc_final: 0.8123 (mm-30) REVERT: A 626 LEU cc_start: 0.9074 (tp) cc_final: 0.8855 (tm) REVERT: A 685 LYS cc_start: 0.8604 (tttp) cc_final: 0.8250 (tptt) REVERT: B 168 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: B 272 MET cc_start: 0.8758 (mmm) cc_final: 0.8483 (mmm) REVERT: B 609 GLU cc_start: 0.8578 (tp30) cc_final: 0.7988 (mm-30) REVERT: C 168 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: C 192 ARG cc_start: 0.6644 (tpm170) cc_final: 0.6410 (tpp-160) REVERT: C 463 MET cc_start: 0.8207 (tpt) cc_final: 0.7990 (tpp) REVERT: C 507 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 602 MET cc_start: 0.9490 (mmm) cc_final: 0.9243 (mmp) REVERT: C 609 GLU cc_start: 0.8571 (tp30) cc_final: 0.8098 (mm-30) REVERT: D 609 GLU cc_start: 0.8565 (tp30) cc_final: 0.8114 (mm-30) outliers start: 51 outliers final: 11 residues processed: 230 average time/residue: 0.5159 time to fit residues: 138.6755 Evaluate side-chains 191 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 183 optimal weight: 40.0000 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.132554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087236 restraints weight = 34981.777| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.54 r_work: 0.3125 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20600 Z= 0.232 Angle : 0.642 6.295 27980 Z= 0.328 Chirality : 0.041 0.147 3176 Planarity : 0.005 0.053 3428 Dihedral : 4.793 46.257 2732 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 2.48 % Allowed : 16.77 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: 0.41 (0.17), residues: 2432 helix: 1.86 (0.14), residues: 1460 sheet: -0.37 (0.53), residues: 84 loop : -2.56 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 307 TYR 0.019 0.002 TYR B 466 PHE 0.019 0.002 PHE C 402 TRP 0.014 0.001 TRP D 173 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (20600) covalent geometry : angle 0.64234 / 0.33 (27980) hydrogen bonds : bond 0.06204 / 4.18 ( 1068) hydrogen bonds : angle 4.24873 / 3.02 ( 3156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.859 Fit side-chains REVERT: A 168 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: A 272 MET cc_start: 0.8740 (mmm) cc_final: 0.8289 (mmm) REVERT: A 602 MET cc_start: 0.9367 (mmm) cc_final: 0.9059 (mmp) REVERT: A 609 GLU cc_start: 0.8501 (tp30) cc_final: 0.8136 (mm-30) REVERT: A 685 LYS cc_start: 0.8499 (tttp) cc_final: 0.8164 (tptt) REVERT: B 168 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: B 192 ARG cc_start: 0.6899 (tpp-160) cc_final: 0.6678 (tpm170) REVERT: B 272 MET cc_start: 0.8783 (mmm) cc_final: 0.8340 (mmm) REVERT: B 276 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 609 GLU cc_start: 0.8486 (tp30) cc_final: 0.8100 (mm-30) REVERT: B 626 LEU cc_start: 0.9221 (tp) cc_final: 0.8913 (mm) REVERT: C 272 MET cc_start: 0.8746 (mmm) cc_final: 0.8313 (mmm) REVERT: C 276 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (mm) REVERT: C 330 TYR cc_start: 0.7538 (t80) cc_final: 0.7293 (t80) REVERT: C 609 GLU cc_start: 0.8533 (tp30) cc_final: 0.8327 (mm-30) REVERT: C 626 LEU cc_start: 0.9216 (tp) cc_final: 0.8908 (mm) REVERT: D 168 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: D 272 MET cc_start: 0.8764 (mmm) cc_final: 0.8308 (mmm) REVERT: D 330 TYR cc_start: 0.7497 (t80) cc_final: 0.7276 (t80) REVERT: D 609 GLU cc_start: 0.8508 (tp30) cc_final: 0.8128 (mm-30) REVERT: D 626 LEU cc_start: 0.9219 (tp) cc_final: 0.8906 (mm) outliers start: 54 outliers final: 14 residues processed: 216 average time/residue: 0.5168 time to fit residues: 129.8690 Evaluate side-chains 187 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 71 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.132348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087187 restraints weight = 34650.665| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.71 r_work: 0.3117 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20600 Z= 0.215 Angle : 0.610 6.853 27980 Z= 0.311 Chirality : 0.040 0.147 3176 Planarity : 0.004 0.054 3428 Dihedral : 4.737 46.485 2732 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 3.12 % Allowed : 17.33 % Favored : 79.55 % 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 are not related in a simple way. whole: 0.53 (0.17), residues: 2432 helix: 1.90 (0.14), residues: 1464 sheet: -0.23 (0.56), residues: 84 loop : -2.43 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 307 TYR 0.018 0.002 TYR D 223 PHE 0.016 0.001 PHE C 486 TRP 0.016 0.001 TRP D 173 HIS 0.003 0.001 HIS D 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (20600) covalent geometry : angle 0.60952 / 0.31 (27980) hydrogen bonds : bond 0.05692 / 3.83 ( 1068) hydrogen bonds : angle 4.15492 / 2.96 ( 3156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 180 time to evaluate : 0.864 Fit side-chains REVERT: A 168 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: A 276 LEU cc_start: 0.8424 (mm) cc_final: 0.8177 (mm) REVERT: A 454 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6851 (mtt90) REVERT: A 602 MET cc_start: 0.9401 (mmm) cc_final: 0.9071 (mmp) REVERT: A 685 LYS cc_start: 0.8550 (tttp) cc_final: 0.8237 (tptt) REVERT: B 168 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: B 272 MET cc_start: 0.8853 (mmm) cc_final: 0.8372 (mmm) REVERT: B 276 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8211 (mm) REVERT: B 454 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6841 (mtt90) REVERT: B 609 GLU cc_start: 0.8358 (tp30) cc_final: 0.8125 (mm-30) REVERT: C 168 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: C 272 MET cc_start: 0.8809 (mmm) cc_final: 0.8551 (mmm) REVERT: C 330 TYR cc_start: 0.7540 (t80) cc_final: 0.7299 (t80) REVERT: C 626 LEU cc_start: 0.9210 (tp) cc_final: 0.8945 (mm) REVERT: D 168 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: D 276 LEU cc_start: 0.8488 (mm) cc_final: 0.8241 (mm) REVERT: D 330 TYR cc_start: 0.7555 (t80) cc_final: 0.7338 (t80) REVERT: D 454 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6885 (mtt90) outliers start: 68 outliers final: 21 residues processed: 225 average time/residue: 0.4996 time to fit residues: 130.8330 Evaluate side-chains 201 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 183 optimal weight: 40.0000 chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090891 restraints weight = 34720.402| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.77 r_work: 0.3173 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20600 Z= 0.123 Angle : 0.536 9.219 27980 Z= 0.271 Chirality : 0.038 0.158 3176 Planarity : 0.003 0.052 3428 Dihedral : 4.523 48.248 2732 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.02 % Allowed : 19.30 % Favored : 78.68 % 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 are not related in a simple way. whole: 0.81 (0.17), residues: 2432 helix: 2.13 (0.14), residues: 1472 sheet: -0.14 (0.56), residues: 84 loop : -2.36 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.019 0.002 TYR A 466 PHE 0.016 0.001 PHE C 486 TRP 0.012 0.001 TRP C 173 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (20600) covalent geometry : angle 0.53553 / 0.27 (27980) hydrogen bonds : bond 0.04276 / 2.87 ( 1068) hydrogen bonds : angle 3.80886 / 2.70 ( 3156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.628 Fit side-chains REVERT: A 168 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 185 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.9001 (m) REVERT: A 602 MET cc_start: 0.9334 (mmm) cc_final: 0.9079 (mmp) REVERT: A 626 LEU cc_start: 0.9089 (tp) cc_final: 0.8850 (mm) REVERT: A 685 LYS cc_start: 0.8561 (tttp) cc_final: 0.8254 (tptt) REVERT: B 168 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: B 272 MET cc_start: 0.8832 (mmm) cc_final: 0.8372 (mmm) REVERT: B 276 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8211 (mm) REVERT: B 609 GLU cc_start: 0.8356 (tp30) cc_final: 0.8060 (mm-30) REVERT: B 626 LEU cc_start: 0.9177 (tp) cc_final: 0.8930 (mm) REVERT: C 168 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: C 230 GLN cc_start: 0.7803 (pt0) cc_final: 0.7447 (pt0) REVERT: C 272 MET cc_start: 0.8777 (mmm) cc_final: 0.8292 (mmm) REVERT: C 276 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8273 (mm) REVERT: C 626 LEU cc_start: 0.9174 (tp) cc_final: 0.8934 (mm) REVERT: C 678 HIS cc_start: 0.7933 (t-90) cc_final: 0.7197 (t-90) REVERT: D 168 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: D 185 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8978 (m) REVERT: D 230 GLN cc_start: 0.7674 (pt0) cc_final: 0.7295 (pt0) REVERT: D 276 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8152 (mm) REVERT: D 626 LEU cc_start: 0.9176 (tp) cc_final: 0.8927 (mm) outliers start: 44 outliers final: 7 residues processed: 225 average time/residue: 0.4363 time to fit residues: 115.8155 Evaluate side-chains 193 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 144 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 238 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.135646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091074 restraints weight = 34811.615| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.54 r_work: 0.3190 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20600 Z= 0.120 Angle : 0.530 8.604 27980 Z= 0.267 Chirality : 0.037 0.161 3176 Planarity : 0.003 0.050 3428 Dihedral : 4.430 49.599 2732 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.53 % Allowed : 18.98 % Favored : 78.49 % 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 are not related in a simple way. whole: 0.94 (0.17), residues: 2432 helix: 2.23 (0.14), residues: 1468 sheet: -0.03 (0.56), residues: 84 loop : -2.29 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 158 TYR 0.022 0.002 TYR A 466 PHE 0.011 0.001 PHE A 389 TRP 0.012 0.001 TRP D 218 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (20600) covalent geometry : angle 0.52991 / 0.27 (27980) hydrogen bonds : bond 0.04191 / 2.82 ( 1068) hydrogen bonds : angle 3.73449 / 2.65 ( 3156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.755 Fit side-chains REVERT: A 168 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: A 185 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9019 (m) REVERT: A 626 LEU cc_start: 0.9079 (tp) cc_final: 0.8848 (mm) REVERT: A 685 LYS cc_start: 0.8602 (tttp) cc_final: 0.8299 (tptt) REVERT: B 168 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: B 272 MET cc_start: 0.8804 (mmm) cc_final: 0.8334 (mmm) REVERT: B 276 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8232 (mm) REVERT: B 609 GLU cc_start: 0.8396 (tp30) cc_final: 0.8088 (mm-30) REVERT: B 626 LEU cc_start: 0.9182 (tp) cc_final: 0.8938 (mm) REVERT: C 230 GLN cc_start: 0.7834 (pt0) cc_final: 0.7466 (pt0) REVERT: C 272 MET cc_start: 0.8795 (mmm) cc_final: 0.8315 (mmm) REVERT: C 276 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8209 (mm) REVERT: C 626 LEU cc_start: 0.9175 (tp) cc_final: 0.8937 (mm) REVERT: C 678 HIS cc_start: 0.7905 (t-90) cc_final: 0.7182 (t-90) REVERT: D 168 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: D 185 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8972 (m) REVERT: D 230 GLN cc_start: 0.7666 (pt0) cc_final: 0.7246 (pt0) REVERT: D 276 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8214 (mm) REVERT: D 626 LEU cc_start: 0.9176 (tp) cc_final: 0.8938 (mm) outliers start: 55 outliers final: 16 residues processed: 225 average time/residue: 0.4940 time to fit residues: 129.2851 Evaluate side-chains 199 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093170 restraints weight = 34802.041| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.55 r_work: 0.3221 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20600 Z= 0.106 Angle : 0.517 8.402 27980 Z= 0.259 Chirality : 0.037 0.164 3176 Planarity : 0.003 0.049 3428 Dihedral : 4.332 50.185 2732 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.47 % Allowed : 20.17 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2432 helix: 2.35 (0.14), residues: 1472 sheet: 0.05 (0.56), residues: 84 loop : -2.28 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 170 TYR 0.024 0.001 TYR B 466 PHE 0.009 0.001 PHE B 389 TRP 0.013 0.001 TRP D 218 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (20600) covalent geometry : angle 0.51734 / 0.26 (27980) hydrogen bonds : bond 0.03669 / 2.46 ( 1068) hydrogen bonds : angle 3.61750 / 2.57 ( 3156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.832 Fit side-chains REVERT: A 168 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 185 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9005 (m) REVERT: A 626 LEU cc_start: 0.9044 (tp) cc_final: 0.8820 (mm) REVERT: A 685 LYS cc_start: 0.8564 (tttp) cc_final: 0.8279 (tptt) REVERT: B 168 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: B 272 MET cc_start: 0.8739 (mmm) cc_final: 0.8272 (mmm) REVERT: B 276 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8202 (mm) REVERT: B 609 GLU cc_start: 0.8417 (tp30) cc_final: 0.8099 (mm-30) REVERT: B 626 LEU cc_start: 0.9153 (tp) cc_final: 0.8930 (mm) REVERT: C 168 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: C 230 GLN cc_start: 0.7848 (pt0) cc_final: 0.7459 (pt0) REVERT: C 272 MET cc_start: 0.8754 (mmm) cc_final: 0.8289 (mmm) REVERT: C 276 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8172 (mm) REVERT: D 168 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: D 185 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8961 (m) REVERT: D 230 GLN cc_start: 0.7634 (pt0) cc_final: 0.7258 (pt0) REVERT: D 276 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8226 (mm) REVERT: D 626 LEU cc_start: 0.9173 (tp) cc_final: 0.8952 (mm) outliers start: 32 outliers final: 11 residues processed: 208 average time/residue: 0.4308 time to fit residues: 105.8085 Evaluate side-chains 198 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 333 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 183 optimal weight: 50.0000 chunk 52 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN B 409 GLN C 409 GLN D 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.131375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086473 restraints weight = 34504.299| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.51 r_work: 0.3111 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20600 Z= 0.228 Angle : 0.626 9.072 27980 Z= 0.317 Chirality : 0.041 0.159 3176 Planarity : 0.004 0.049 3428 Dihedral : 4.644 50.190 2732 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 1.47 % Allowed : 20.50 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2432 helix: 2.12 (0.13), residues: 1464 sheet: 0.01 (0.57), residues: 84 loop : -2.29 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 307 TYR 0.024 0.002 TYR B 466 PHE 0.017 0.002 PHE D 598 TRP 0.014 0.001 TRP D 173 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (20600) covalent geometry : angle 0.62642 / 0.32 (27980) hydrogen bonds : bond 0.05873 / 3.96 ( 1068) hydrogen bonds : angle 4.14808 / 2.96 ( 3156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 1.090 Fit side-chains REVERT: A 168 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: A 602 MET cc_start: 0.9338 (mmm) cc_final: 0.9106 (mmp) REVERT: A 685 LYS cc_start: 0.8588 (tttp) cc_final: 0.8317 (tptt) REVERT: B 168 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: B 272 MET cc_start: 0.8791 (mmm) cc_final: 0.8391 (mmm) REVERT: B 276 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8256 (mm) REVERT: B 460 ILE cc_start: 0.6797 (pt) cc_final: 0.6447 (mp) REVERT: B 609 GLU cc_start: 0.8411 (tp30) cc_final: 0.8211 (mm-30) REVERT: C 168 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: C 230 GLN cc_start: 0.7708 (pt0) cc_final: 0.7328 (pt0) REVERT: C 272 MET cc_start: 0.8813 (mmm) cc_final: 0.8440 (mmm) REVERT: C 276 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8214 (mm) REVERT: D 168 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: D 230 GLN cc_start: 0.7661 (pt0) cc_final: 0.7364 (pt0) outliers start: 32 outliers final: 17 residues processed: 200 average time/residue: 0.4931 time to fit residues: 115.6388 Evaluate side-chains 189 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090618 restraints weight = 34691.682| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.61 r_work: 0.3178 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20600 Z= 0.119 Angle : 0.550 9.151 27980 Z= 0.275 Chirality : 0.038 0.158 3176 Planarity : 0.003 0.047 3428 Dihedral : 4.479 50.348 2732 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.83 % Allowed : 21.46 % Favored : 77.71 % 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 are not related in a simple way. whole: 1.05 (0.17), residues: 2432 helix: 2.28 (0.14), residues: 1468 sheet: 0.13 (0.57), residues: 84 loop : -2.17 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 170 TYR 0.018 0.001 TYR B 466 PHE 0.011 0.001 PHE A 389 TRP 0.014 0.001 TRP D 218 HIS 0.003 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (20600) covalent geometry : angle 0.55000 / 0.28 (27980) hydrogen bonds : bond 0.04074 / 2.74 ( 1068) hydrogen bonds : angle 3.78027 / 2.68 ( 3156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.786 Fit side-chains REVERT: A 168 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: A 685 LYS cc_start: 0.8593 (tttp) cc_final: 0.8379 (tptt) REVERT: B 168 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: B 272 MET cc_start: 0.8797 (mmm) cc_final: 0.8421 (mmm) REVERT: B 276 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8224 (mm) REVERT: B 460 ILE cc_start: 0.7007 (pt) cc_final: 0.6638 (mp) REVERT: B 609 GLU cc_start: 0.8436 (tp30) cc_final: 0.8117 (mm-30) REVERT: C 168 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: C 230 GLN cc_start: 0.7705 (pt0) cc_final: 0.7407 (pt0) REVERT: C 272 MET cc_start: 0.8808 (mmm) cc_final: 0.8328 (mmm) REVERT: C 276 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8211 (mm) REVERT: D 168 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: D 230 GLN cc_start: 0.7707 (pt0) cc_final: 0.7374 (pt0) outliers start: 18 outliers final: 12 residues processed: 189 average time/residue: 0.4988 time to fit residues: 110.1841 Evaluate side-chains 191 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 50 optimal weight: 0.0270 chunk 233 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 196 optimal weight: 0.0010 chunk 186 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 0.9046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.136343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092324 restraints weight = 34603.465| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.51 r_work: 0.3209 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20600 Z= 0.109 Angle : 0.527 8.865 27980 Z= 0.265 Chirality : 0.037 0.164 3176 Planarity : 0.003 0.045 3428 Dihedral : 4.316 50.623 2732 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.29 % Allowed : 20.86 % Favored : 77.85 % 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 are not related in a simple way. whole: 1.22 (0.17), residues: 2432 helix: 2.43 (0.14), residues: 1468 sheet: 0.20 (0.56), residues: 84 loop : -2.15 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 307 TYR 0.023 0.001 TYR B 466 PHE 0.009 0.001 PHE B 389 TRP 0.019 0.001 TRP D 218 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20600) covalent geometry : angle 0.52696 / 0.26 (27980) hydrogen bonds : bond 0.03709 / 2.50 ( 1068) hydrogen bonds : angle 3.63162 / 2.57 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9042.33 seconds wall clock time: 154 minutes 13.05 seconds (9253.05 seconds total)