Starting phenix.real_space_refine on Thu Mar 5 06:46:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xer_33158/03_2026/7xer_33158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xer_33158/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xer_33158/03_2026/7xer_33158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xer_33158/03_2026/7xer_33158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xer_33158/03_2026/7xer_33158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xer_33158/03_2026/7xer_33158.map" } 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-5986/lib/python3.9/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: 4.65, per 1000 atoms: 0.23 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: 1.70 Conformation dependent library (CDL) restraints added in 952.9 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: 0.56 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: 3.05 Time building geometry restraints manager: 2.30 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: 11070 16.47 - 32.95: 993 32.95 - 49.42: 156 49.42 - 65.89: 33 65.89 - 82.37: 24 Dihedral angle restraints: 12276 sinusoidal: 5108 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 12273 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: 0.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.770 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 13.071 82.366 7652 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 covalent geometry : bond 0.00317 (20600) covalent geometry : angle 0.74295 (27980) hydrogen bonds : bond 0.15700 ( 1068) hydrogen bonds : angle 5.03522 ( 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 : 0.714 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: 0.6361 time to fit residues: 247.9236 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 : 0.696 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.137931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093306 restraints weight = 35092.935| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.86 r_work: 0.3207 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1747 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= 0.151 Angle : 0.613 5.609 27980 Z= 0.312 Chirality : 0.039 0.155 3176 Planarity : 0.004 0.051 3428 Dihedral : 5.678 55.622 2956 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.03 % Allowed : 10.20 % 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: 0.26 (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 covalent geometry : bond 0.00347 (20600) covalent geometry : angle 0.61306 (27980) hydrogen bonds : bond 0.05062 ( 1068) hydrogen bonds : angle 4.08613 ( 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 300 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.6885 (tpm170) cc_final: 0.6682 (tpp-160) REVERT: A 609 GLU cc_start: 0.8558 (tp30) cc_final: 0.8044 (mm-30) REVERT: A 685 LYS cc_start: 0.8562 (tttp) cc_final: 0.8245 (tptt) REVERT: B 192 ARG cc_start: 0.6921 (tpm170) cc_final: 0.6692 (tpp-160) REVERT: B 609 GLU cc_start: 0.8536 (tp30) cc_final: 0.8005 (mm-30) 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: 0.8034 (mm-30) REVERT: D 434 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8736 (mp) REVERT: D 602 MET cc_start: 0.9447 (mmm) cc_final: 0.9193 (mmp) REVERT: D 609 GLU cc_start: 0.8539 (tp30) cc_final: 0.8017 (mm-30) outliers start: 66 outliers final: 12 residues processed: 265 average time/residue: 0.5288 time to fit residues: 161.8149 Evaluate side-chains 216 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 B residue 483 VAL 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 Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 0.0030 chunk 120 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 231 optimal weight: 0.2980 chunk 182 optimal weight: 7.9990 chunk 205 optimal weight: 0.1980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.141350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097470 restraints weight = 35287.088| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.81 r_work: 0.3285 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1888 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= 0.105 Angle : 0.517 5.140 27980 Z= 0.264 Chirality : 0.037 0.167 3176 Planarity : 0.003 0.047 3428 Dihedral : 5.144 51.611 2956 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.21 % Allowed : 14.61 % Favored : 83.18 % 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: 0.62 (0.17), residues: 2432 helix: 1.99 (0.14), residues: 1464 sheet: -0.10 (0.52), residues: 84 loop : -2.43 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 158 TYR 0.018 0.001 TYR B 466 PHE 0.013 0.001 PHE C 467 TRP 0.010 0.001 TRP C 504 HIS 0.004 0.001 HIS D 229 Details of bonding type rmsd covalent geometry : bond 0.00214 (20600) covalent geometry : angle 0.51749 (27980) hydrogen bonds : bond 0.03719 ( 1068) hydrogen bonds : angle 3.68416 ( 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 274 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.733 Fit side-chains REVERT: A 192 ARG cc_start: 0.6859 (tpm170) cc_final: 0.6573 (tpp-160) REVERT: A 272 MET cc_start: 0.8761 (mmm) cc_final: 0.8506 (mmm) REVERT: A 463 MET cc_start: 0.8181 (tpt) cc_final: 0.7934 (tpp) REVERT: A 507 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 609 GLU cc_start: 0.8550 (tp30) cc_final: 0.8043 (mm-30) REVERT: A 626 LEU cc_start: 0.8994 (tp) cc_final: 0.8786 (tm) REVERT: A 685 LYS cc_start: 0.8576 (tttp) cc_final: 0.8279 (tptt) REVERT: B 192 ARG cc_start: 0.6860 (tpm170) cc_final: 0.6571 (tpp-160) REVERT: B 272 MET cc_start: 0.8793 (mmm) cc_final: 0.8543 (mmm) REVERT: B 507 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (tt) REVERT: B 609 GLU cc_start: 0.8594 (tp30) cc_final: 0.8060 (mm-30) REVERT: B 626 LEU cc_start: 0.9005 (tp) cc_final: 0.8786 (tm) REVERT: C 463 MET cc_start: 0.8205 (tpt) cc_final: 0.7951 (tpp) REVERT: C 602 MET cc_start: 0.9449 (mmm) cc_final: 0.9080 (mmp) REVERT: C 609 GLU cc_start: 0.8546 (tp30) cc_final: 0.8075 (mm-30) REVERT: C 626 LEU cc_start: 0.9021 (tp) cc_final: 0.8818 (tm) REVERT: D 272 MET cc_start: 0.8696 (mmm) cc_final: 0.8449 (mmm) REVERT: D 463 MET cc_start: 0.8226 (tpt) cc_final: 0.8025 (tpp) REVERT: D 507 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 609 GLU cc_start: 0.8534 (tp30) cc_final: 0.8028 (mm-30) REVERT: D 626 LEU cc_start: 0.8981 (tp) cc_final: 0.8759 (tm) outliers start: 48 outliers final: 10 residues processed: 248 average time/residue: 0.4612 time to fit residues: 133.9725 Evaluate side-chains 201 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 507 LEU 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: 6.9990 chunk 89 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 183 optimal weight: 40.0000 chunk 179 optimal weight: 0.0020 chunk 219 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.134414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089245 restraints weight = 34976.865| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.55 r_work: 0.3156 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20600 Z= 0.188 Angle : 0.590 6.109 27980 Z= 0.303 Chirality : 0.040 0.159 3176 Planarity : 0.004 0.051 3428 Dihedral : 5.217 48.133 2956 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.70 % Rotamer: Outliers : 2.62 % Allowed : 16.68 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2432 helix: 1.96 (0.14), residues: 1468 sheet: -0.28 (0.52), residues: 84 loop : -2.47 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 307 TYR 0.019 0.002 TYR B 466 PHE 0.016 0.001 PHE C 402 TRP 0.012 0.001 TRP D 173 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00444 (20600) covalent geometry : angle 0.58969 (27980) hydrogen bonds : bond 0.05497 ( 1068) hydrogen bonds : angle 4.05664 ( 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 251 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.736 Fit side-chains REVERT: A 168 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: A 272 MET cc_start: 0.8773 (mmm) cc_final: 0.8288 (mmm) REVERT: A 276 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8268 (mm) REVERT: A 330 TYR cc_start: 0.7458 (t80) cc_final: 0.7247 (t80) REVERT: A 602 MET cc_start: 0.9385 (mmm) cc_final: 0.9110 (mmp) REVERT: A 609 GLU cc_start: 0.8520 (tp30) cc_final: 0.8147 (mm-30) REVERT: A 685 LYS cc_start: 0.8504 (tttp) cc_final: 0.8164 (tptt) REVERT: B 168 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: B 272 MET cc_start: 0.8762 (mmm) cc_final: 0.8265 (mmm) REVERT: B 276 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8301 (mm) REVERT: B 330 TYR cc_start: 0.7356 (t80) cc_final: 0.7136 (t80) REVERT: B 609 GLU cc_start: 0.8428 (tp30) cc_final: 0.8021 (mm-30) REVERT: C 168 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: C 192 ARG cc_start: 0.7031 (tpp-160) cc_final: 0.6809 (tpm170) REVERT: C 609 GLU cc_start: 0.8538 (tp30) cc_final: 0.8124 (mm-30) REVERT: D 168 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: D 272 MET cc_start: 0.8751 (mmm) cc_final: 0.8257 (mmm) REVERT: D 276 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8310 (mm) REVERT: D 330 TYR cc_start: 0.7449 (t80) cc_final: 0.7229 (t80) REVERT: D 609 GLU cc_start: 0.8410 (tp30) cc_final: 0.8138 (mm-30) outliers start: 57 outliers final: 20 residues processed: 226 average time/residue: 0.4892 time to fit residues: 128.5918 Evaluate side-chains 200 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 649 THR 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 438 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU 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 649 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU 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 649 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 71 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS D 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091086 restraints weight = 34618.815| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.75 r_work: 0.3178 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20600 Z= 0.137 Angle : 0.539 6.640 27980 Z= 0.274 Chirality : 0.038 0.164 3176 Planarity : 0.003 0.051 3428 Dihedral : 5.032 47.856 2956 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.53 % Allowed : 18.66 % Favored : 78.81 % 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: 0.79 (0.17), residues: 2432 helix: 2.14 (0.14), residues: 1464 sheet: -0.18 (0.54), residues: 84 loop : -2.38 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 307 TYR 0.017 0.002 TYR B 466 PHE 0.015 0.001 PHE C 486 TRP 0.015 0.001 TRP D 173 HIS 0.003 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00318 (20600) covalent geometry : angle 0.53882 (27980) hydrogen bonds : bond 0.04465 ( 1068) hydrogen bonds : angle 3.85180 ( 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 239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.790 Fit side-chains REVERT: A 168 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: A 272 MET cc_start: 0.8837 (mmm) cc_final: 0.8379 (mmm) REVERT: A 276 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (mm) REVERT: A 602 MET cc_start: 0.9366 (mmm) cc_final: 0.9107 (mmp) REVERT: A 609 GLU cc_start: 0.8394 (tp30) cc_final: 0.8092 (mm-30) REVERT: A 626 LEU cc_start: 0.9102 (tp) cc_final: 0.8820 (mm) REVERT: A 685 LYS cc_start: 0.8551 (tttp) cc_final: 0.8244 (tptt) REVERT: B 117 MET cc_start: 0.8404 (mtt) cc_final: 0.8114 (mtt) REVERT: B 168 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: B 272 MET cc_start: 0.8779 (mmm) cc_final: 0.8264 (mmm) REVERT: B 276 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 507 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 609 GLU cc_start: 0.8345 (tp30) cc_final: 0.8105 (mm-30) REVERT: B 626 LEU cc_start: 0.9099 (tp) cc_final: 0.8816 (mm) REVERT: C 272 MET cc_start: 0.8796 (mmm) cc_final: 0.8260 (mmm) REVERT: C 609 GLU cc_start: 0.8419 (tp30) cc_final: 0.8091 (mm-30) REVERT: C 626 LEU cc_start: 0.9106 (tp) cc_final: 0.8827 (mm) REVERT: D 168 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: D 272 MET cc_start: 0.8811 (mmm) cc_final: 0.8289 (mmm) REVERT: D 276 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8206 (mm) REVERT: D 609 GLU cc_start: 0.8377 (tp30) cc_final: 0.8076 (mm-30) REVERT: D 626 LEU cc_start: 0.9106 (tp) cc_final: 0.8822 (mm) outliers start: 55 outliers final: 12 residues processed: 225 average time/residue: 0.4886 time to fit residues: 127.7346 Evaluate side-chains 194 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 LEU 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 507 LEU Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 333 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 276 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 438 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 183 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.133740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088767 restraints weight = 34755.878| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.73 r_work: 0.3144 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20600 Z= 0.177 Angle : 0.571 6.450 27980 Z= 0.291 Chirality : 0.039 0.160 3176 Planarity : 0.004 0.052 3428 Dihedral : 5.028 48.841 2956 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.12 % Allowed : 18.89 % Favored : 77.99 % 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: 0.74 (0.17), residues: 2432 helix: 2.09 (0.14), residues: 1468 sheet: -0.13 (0.55), residues: 84 loop : -2.40 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 307 TYR 0.019 0.002 TYR B 466 PHE 0.016 0.001 PHE C 486 TRP 0.010 0.001 TRP B 173 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00424 (20600) covalent geometry : angle 0.57094 (27980) hydrogen bonds : bond 0.05199 ( 1068) hydrogen bonds : angle 3.95681 ( 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 261 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 0.878 Fit side-chains REVERT: A 168 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: A 272 MET cc_start: 0.8821 (mmm) cc_final: 0.8452 (mmm) REVERT: A 276 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8205 (mm) REVERT: A 454 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6786 (mtt90) REVERT: A 602 MET cc_start: 0.9359 (mmm) cc_final: 0.9102 (mmp) REVERT: A 609 GLU cc_start: 0.8442 (tp30) cc_final: 0.8154 (mm-30) REVERT: A 626 LEU cc_start: 0.9143 (tp) cc_final: 0.8875 (mm) REVERT: A 685 LYS cc_start: 0.8575 (tttp) cc_final: 0.8261 (tptt) REVERT: B 168 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: B 272 MET cc_start: 0.8817 (mmm) cc_final: 0.8334 (mmm) REVERT: B 276 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 454 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6838 (mtt90) REVERT: B 609 GLU cc_start: 0.8337 (tp30) cc_final: 0.8055 (mm-30) REVERT: B 626 LEU cc_start: 0.9139 (tp) cc_final: 0.8867 (mm) REVERT: C 230 GLN cc_start: 0.7886 (pt0) cc_final: 0.7536 (pt0) REVERT: C 454 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.6812 (mtt90) REVERT: C 626 LEU cc_start: 0.9142 (tp) cc_final: 0.8879 (mm) REVERT: D 168 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: D 230 GLN cc_start: 0.7887 (pt0) cc_final: 0.7512 (pt0) REVERT: D 272 MET cc_start: 0.8808 (mmm) cc_final: 0.8322 (mmm) REVERT: D 276 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8223 (mm) REVERT: D 454 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6785 (mtt90) REVERT: D 609 GLU cc_start: 0.8445 (tp30) cc_final: 0.8156 (mm-30) REVERT: D 626 LEU cc_start: 0.9141 (tp) cc_final: 0.8867 (mm) outliers start: 68 outliers final: 23 residues processed: 235 average time/residue: 0.5466 time to fit residues: 148.1260 Evaluate side-chains 215 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 276 LEU 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 649 THR 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 379 GLU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 144 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 156 optimal weight: 0.0010 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091357 restraints weight = 34789.940| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.54 r_work: 0.3187 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20600 Z= 0.124 Angle : 0.543 9.200 27980 Z= 0.273 Chirality : 0.038 0.276 3176 Planarity : 0.003 0.051 3428 Dihedral : 4.870 49.960 2956 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.98 % Allowed : 19.67 % 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: 0.92 (0.17), residues: 2432 helix: 2.23 (0.14), residues: 1468 sheet: -0.06 (0.55), residues: 84 loop : -2.33 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 275 TYR 0.020 0.002 TYR B 466 PHE 0.017 0.001 PHE C 486 TRP 0.012 0.001 TRP C 218 HIS 0.002 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00284 (20600) covalent geometry : angle 0.54250 (27980) hydrogen bonds : bond 0.04224 ( 1068) hydrogen bonds : angle 3.77950 ( 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 237 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.726 Fit side-chains REVERT: A 168 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 272 MET cc_start: 0.8794 (mmm) cc_final: 0.8519 (mmm) REVERT: A 609 GLU cc_start: 0.8415 (tp30) cc_final: 0.8107 (mm-30) REVERT: A 626 LEU cc_start: 0.9115 (tp) cc_final: 0.8877 (mm) REVERT: A 685 LYS cc_start: 0.8548 (tttp) cc_final: 0.8243 (tptt) REVERT: B 168 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: B 272 MET cc_start: 0.8762 (mmm) cc_final: 0.8293 (mmm) REVERT: B 276 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8224 (mm) REVERT: B 609 GLU cc_start: 0.8351 (tp30) cc_final: 0.8073 (mm-30) REVERT: B 626 LEU cc_start: 0.9120 (tp) cc_final: 0.8878 (mm) REVERT: C 161 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 230 GLN cc_start: 0.7896 (pt0) cc_final: 0.7530 (pt0) REVERT: C 272 MET cc_start: 0.8546 (mmm) cc_final: 0.7871 (tpt) REVERT: C 626 LEU cc_start: 0.9120 (tp) cc_final: 0.8880 (mm) REVERT: D 168 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: D 230 GLN cc_start: 0.7870 (pt0) cc_final: 0.7470 (pt0) REVERT: D 272 MET cc_start: 0.8787 (mmm) cc_final: 0.8331 (mmm) REVERT: D 276 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8227 (mm) REVERT: D 454 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6712 (mtt90) REVERT: D 609 GLU cc_start: 0.8403 (tp30) cc_final: 0.8099 (mm-30) REVERT: D 626 LEU cc_start: 0.9123 (tp) cc_final: 0.8880 (mm) outliers start: 43 outliers final: 12 residues processed: 224 average time/residue: 0.4865 time to fit residues: 127.2458 Evaluate side-chains 195 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 666 MET 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 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 161 SER 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 D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 241 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.137227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093009 restraints weight = 34787.440| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.56 r_work: 0.3217 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20600 Z= 0.109 Angle : 0.525 8.963 27980 Z= 0.263 Chirality : 0.037 0.260 3176 Planarity : 0.003 0.049 3428 Dihedral : 4.727 50.916 2956 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.61 % Allowed : 20.82 % Favored : 77.57 % 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: 1.03 (0.17), residues: 2432 helix: 2.29 (0.14), residues: 1476 sheet: 0.03 (0.55), residues: 84 loop : -2.27 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 454 TYR 0.022 0.001 TYR B 466 PHE 0.017 0.001 PHE C 486 TRP 0.013 0.001 TRP D 218 HIS 0.002 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00243 (20600) covalent geometry : angle 0.52464 (27980) hydrogen bonds : bond 0.03825 ( 1068) hydrogen bonds : angle 3.65221 ( 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 225 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.840 Fit side-chains REVERT: A 168 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 272 MET cc_start: 0.8740 (mmm) cc_final: 0.8280 (mmm) REVERT: A 276 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 626 LEU cc_start: 0.9067 (tp) cc_final: 0.8837 (mm) REVERT: A 685 LYS cc_start: 0.8555 (tttp) cc_final: 0.8250 (tptt) REVERT: B 168 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 272 MET cc_start: 0.8782 (mmm) cc_final: 0.8324 (mmm) REVERT: B 276 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 609 GLU cc_start: 0.8405 (tp30) cc_final: 0.8098 (mm-30) REVERT: B 626 LEU cc_start: 0.9071 (tp) cc_final: 0.8839 (mm) REVERT: C 168 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: C 230 GLN cc_start: 0.7911 (pt0) cc_final: 0.7573 (pt0) REVERT: C 272 MET cc_start: 0.8450 (mmm) cc_final: 0.7776 (tpt) REVERT: C 626 LEU cc_start: 0.9062 (tp) cc_final: 0.8829 (mm) REVERT: D 230 GLN cc_start: 0.7799 (pt0) cc_final: 0.7402 (pt0) REVERT: D 272 MET cc_start: 0.8776 (mmm) cc_final: 0.8313 (mmm) REVERT: D 276 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8205 (mm) REVERT: D 626 LEU cc_start: 0.9071 (tp) cc_final: 0.8837 (mm) outliers start: 35 outliers final: 11 residues processed: 213 average time/residue: 0.5030 time to fit residues: 124.8160 Evaluate side-chains 199 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 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 276 LEU 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 333 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 183 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087022 restraints weight = 34560.787| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.50 r_work: 0.3121 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20600 Z= 0.216 Angle : 0.617 9.085 27980 Z= 0.312 Chirality : 0.040 0.182 3176 Planarity : 0.004 0.050 3428 Dihedral : 4.960 51.469 2956 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.84 % Allowed : 20.59 % Favored : 77.57 % 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: 2.14 (0.14), residues: 1464 sheet: -0.00 (0.55), residues: 84 loop : -2.34 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 307 TYR 0.022 0.002 TYR B 466 PHE 0.018 0.002 PHE C 486 TRP 0.013 0.001 TRP B 173 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00517 (20600) covalent geometry : angle 0.61699 (27980) hydrogen bonds : bond 0.05780 ( 1068) hydrogen bonds : angle 4.14039 ( 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 213 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.755 Fit side-chains REVERT: A 134 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 168 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: A 272 MET cc_start: 0.8781 (mmm) cc_final: 0.8379 (mmm) REVERT: A 276 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8206 (mm) REVERT: A 685 LYS cc_start: 0.8548 (tttp) cc_final: 0.8250 (tptt) REVERT: B 168 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: B 272 MET cc_start: 0.8765 (mmm) cc_final: 0.8362 (mmm) REVERT: B 276 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8236 (mm) REVERT: C 168 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: C 230 GLN cc_start: 0.7817 (pt0) cc_final: 0.7451 (pt0) REVERT: C 678 HIS cc_start: 0.7965 (t-90) cc_final: 0.7222 (t-90) REVERT: D 168 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: D 230 GLN cc_start: 0.7699 (pt0) cc_final: 0.7310 (pt0) REVERT: D 272 MET cc_start: 0.8793 (mmm) cc_final: 0.8394 (mmm) REVERT: D 276 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8240 (mm) outliers start: 40 outliers final: 21 residues processed: 201 average time/residue: 0.5413 time to fit residues: 125.7993 Evaluate side-chains 191 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 649 THR 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 492 TYR Chi-restraints excluded: chain B residue 649 THR 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 333 VAL 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 276 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 649 THR 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: 0.5980 chunk 65 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 196 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.136874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092869 restraints weight = 34809.583| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.61 r_work: 0.3213 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20600 Z= 0.106 Angle : 0.525 8.631 27980 Z= 0.262 Chirality : 0.037 0.175 3176 Planarity : 0.003 0.047 3428 Dihedral : 4.725 52.170 2956 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.15 % Allowed : 21.65 % Favored : 77.21 % 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: 1.14 (0.17), residues: 2432 helix: 2.37 (0.14), residues: 1468 sheet: 0.15 (0.55), residues: 84 loop : -2.18 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 512 TYR 0.019 0.001 TYR B 466 PHE 0.018 0.001 PHE C 486 TRP 0.015 0.001 TRP C 218 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00231 (20600) covalent geometry : angle 0.52538 (27980) hydrogen bonds : bond 0.03651 ( 1068) hydrogen bonds : angle 3.69022 ( 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 214 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.740 Fit side-chains REVERT: A 168 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: A 192 ARG cc_start: 0.6447 (tpm170) cc_final: 0.6217 (tpp-160) REVERT: A 276 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 626 LEU cc_start: 0.9095 (tp) cc_final: 0.8877 (mm) REVERT: A 685 LYS cc_start: 0.8599 (tttp) cc_final: 0.8367 (tptt) REVERT: B 168 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: B 192 ARG cc_start: 0.6468 (tpm170) cc_final: 0.6233 (tpp-160) REVERT: B 272 MET cc_start: 0.8777 (mmm) cc_final: 0.8331 (mmm) REVERT: B 276 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 626 LEU cc_start: 0.9076 (tp) cc_final: 0.8847 (mm) REVERT: C 230 GLN cc_start: 0.7886 (pt0) cc_final: 0.7528 (pt0) REVERT: C 602 MET cc_start: 0.9403 (mmm) cc_final: 0.9076 (mmp) REVERT: C 626 LEU cc_start: 0.9105 (tp) cc_final: 0.8890 (mm) REVERT: C 678 HIS cc_start: 0.7915 (t-90) cc_final: 0.7157 (t-90) REVERT: D 168 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: D 230 GLN cc_start: 0.7723 (pt0) cc_final: 0.7382 (pt0) REVERT: D 272 MET cc_start: 0.8786 (mmm) cc_final: 0.8340 (mmm) REVERT: D 276 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 626 LEU cc_start: 0.9073 (tp) cc_final: 0.8849 (mm) outliers start: 25 outliers final: 11 residues processed: 205 average time/residue: 0.4747 time to fit residues: 114.6787 Evaluate side-chains 192 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain A residue 333 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 702 VAL Chi-restraints excluded: chain C residue 157 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 276 LEU 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: 6.9990 chunk 233 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 196 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 409 GLN D 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.135278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090888 restraints weight = 34581.089| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.51 r_work: 0.3187 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3091 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= 0.127 Angle : 0.547 10.409 27980 Z= 0.272 Chirality : 0.038 0.172 3176 Planarity : 0.003 0.045 3428 Dihedral : 4.690 52.066 2956 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.83 % Allowed : 22.06 % Favored : 77.11 % 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: 1.13 (0.17), residues: 2432 helix: 2.33 (0.14), residues: 1472 sheet: 0.15 (0.55), residues: 84 loop : -2.14 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.022 0.002 TYR B 466 PHE 0.017 0.001 PHE C 486 TRP 0.014 0.001 TRP C 218 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00296 (20600) covalent geometry : angle 0.54669 (27980) hydrogen bonds : bond 0.04194 ( 1068) hydrogen bonds : angle 3.77031 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9445.81 seconds wall clock time: 160 minutes 49.46 seconds (9649.46 seconds total)