Starting phenix.real_space_refine on Fri Jul 3 03:34:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.map" model { file = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2026/8otw_17185.cif" } resolution = 3.68 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 60 5.16 5 C 7525 2.51 5 N 1935 2.21 5 O 2049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11571 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6102 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 25, 'TRANS': 807} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "A" Number of atoms: 5383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5383 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 20, 'TRANS': 668} Chain breaks: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 2.64, per 1000 atoms: 0.23 Number of scatterers: 11571 At special positions: 0 Unit cell: (102.66, 133.558, 107.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 2 15.00 O 2049 8.00 N 1935 7.00 C 7525 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: 0.93 Conformation dependent library (CDL) restraints added in 619.3 milliseconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2862 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 76 through 95 removed outlier: 4.366A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.238A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.859A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 removed outlier: 3.660A pdb=" N VAL B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.886A pdb=" N ASN B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.603A pdb=" N LEU B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.668A pdb=" N SER B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.508A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 413 removed outlier: 4.457A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.546A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 452 through 482 removed outlier: 3.899A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.661A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 600 removed outlier: 3.848A pdb=" N MET B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.582A pdb=" N ILE B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 654 Processing helix chain 'B' and resid 668 through 677 Processing helix chain 'B' and resid 677 through 704 removed outlier: 4.077A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 724 through 750 removed outlier: 3.898A pdb=" N ILE B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 730 " --> pdb=" O GLN B 726 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 761 removed outlier: 3.558A pdb=" N ILE B 759 " --> pdb=" O GLY B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 784 removed outlier: 4.401A pdb=" N ASP B 767 " --> pdb=" O TRP B 763 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 770 " --> pdb=" O PHE B 766 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 771 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 removed outlier: 3.621A pdb=" N LEU B 805 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 812 Processing helix chain 'B' and resid 813 through 855 removed outlier: 3.787A pdb=" N LEU B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 3.835A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 4.108A pdb=" N LYS B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.308A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 Processing helix chain 'A' and resid 76 through 95 removed outlier: 4.533A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.329A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 removed outlier: 3.639A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.725A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.830A pdb=" N ARG A 161 " --> pdb=" O HIS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.634A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.682A pdb=" N VAL A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 250 removed outlier: 3.649A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.510A pdb=" N SER A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.653A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 344 through 375 removed outlier: 3.821A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 413 removed outlier: 4.073A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 removed outlier: 3.630A pdb=" N ALA A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.841A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 482 removed outlier: 3.958A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.772A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 577 through 600 removed outlier: 3.967A pdb=" N LYS A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP A 595 " --> pdb=" O LYS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 621 removed outlier: 3.976A pdb=" N ARG A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 Processing helix chain 'A' and resid 642 through 654 Processing helix chain 'A' and resid 816 through 854 removed outlier: 3.873A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.919A pdb=" N GLU A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.343A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 943 removed outlier: 3.555A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2598 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: 1.56 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1869 1.31 - 1.44: 2905 1.44 - 1.57: 6887 1.57 - 1.69: 4 1.69 - 1.82: 112 Bond restraints: 11777 Sorted by residual: bond pdb=" C11 CPL A1401 " pdb=" O3 CPL A1401 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C11 CPL B1401 " pdb=" O3 CPL B1401 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C31 CPL A1401 " pdb=" O2 CPL A1401 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C31 CPL B1401 " pdb=" O2 CPL B1401 " ideal model delta sigma weight residual 1.332 1.413 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C43 CPL A1401 " pdb=" C44 CPL A1401 " ideal model delta sigma weight residual 1.496 1.548 -0.052 2.00e-02 2.50e+03 6.78e+00 ... (remaining 11772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 15920 5.16 - 10.31: 61 10.31 - 15.47: 4 15.47 - 20.63: 3 20.63 - 25.78: 2 Bond angle restraints: 15990 Sorted by residual: angle pdb=" C39 CPL A1401 " pdb=" C40 CPL A1401 " pdb=" C41 CPL A1401 " ideal model delta sigma weight residual 127.51 153.29 -25.78 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " pdb=" C41 CPL B1401 " ideal model delta sigma weight residual 127.51 152.55 -25.04 3.00e+00 1.11e-01 6.96e+01 angle pdb=" O3P CPL A1401 " pdb=" P CPL A1401 " pdb=" O4P CPL A1401 " ideal model delta sigma weight residual 93.29 109.75 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3P CPL B1401 " pdb=" P CPL B1401 " pdb=" O4P CPL B1401 " ideal model delta sigma weight residual 93.29 109.69 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C38 CPL B1401 " pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " ideal model delta sigma weight residual 127.82 111.48 16.34 3.00e+00 1.11e-01 2.97e+01 ... (remaining 15985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 6288 22.94 - 45.87: 650 45.87 - 68.81: 64 68.81 - 91.75: 24 91.75 - 114.69: 2 Dihedral angle restraints: 7028 sinusoidal: 2618 harmonic: 4410 Sorted by residual: dihedral pdb=" CA ILE B 78 " pdb=" C ILE B 78 " pdb=" N VAL B 79 " pdb=" CA VAL B 79 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ARG A 875 " pdb=" C ARG A 875 " pdb=" N LEU A 876 " pdb=" CA LEU A 876 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" N CPL A1401 " pdb=" C4 CPL A1401 " pdb=" C5 CPL A1401 " pdb=" O4P CPL A1401 " ideal model delta sinusoidal sigma weight residual 288.92 174.23 114.69 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 7025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1522 0.048 - 0.095: 360 0.095 - 0.143: 53 0.143 - 0.191: 0 0.191 - 0.238: 3 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C2 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C3 CPL A1401 " pdb=" O2 CPL A1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C3 CPL B1401 " pdb=" O2 CPL B1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA GLU A 911 " pdb=" N GLU A 911 " pdb=" C GLU A 911 " pdb=" CB GLU A 911 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1935 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 642 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 352 " -0.018 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE A 352 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 352 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 352 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 352 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 352 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 352 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 643 " -0.012 2.00e-02 2.50e+03 1.22e-02 3.71e+00 pdb=" CG TRP A 643 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 643 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 643 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 643 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 643 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 643 " 0.000 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 266 2.70 - 3.25: 12672 3.25 - 3.80: 19212 3.80 - 4.35: 22096 4.35 - 4.90: 36367 Nonbonded interactions: 90613 Sorted by model distance: nonbonded pdb=" O ILE B 81 " pdb=" OG SER B 84 " model vdw 2.149 3.040 nonbonded pdb=" O GLY B 369 " pdb=" OG1 THR B 373 " model vdw 2.185 3.040 nonbonded pdb=" O MET B 133 " pdb=" ND2 ASN B 444 " model vdw 2.212 3.120 nonbonded pdb=" OG SER A 593 " pdb=" NE2 GLN A 597 " model vdw 2.246 3.120 nonbonded pdb=" N GLU B 344 " pdb=" OE1 GLU B 344 " model vdw 2.249 3.120 ... (remaining 90608 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.004 0.088 11777 Z= 0.189 Angle : 0.854 25.785 15990 Z= 0.384 Chirality : 0.040 0.238 1938 Planarity : 0.004 0.062 1985 Dihedral : 17.682 114.686 4166 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.09 % Allowed : 35.19 % Favored : 64.73 % 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: 1.81 (0.23), residues: 1510 helix: 1.79 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.62 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.010 0.001 TYR B 387 PHE 0.042 0.001 PHE A 352 TRP 0.033 0.001 TRP A 643 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (11777) covalent geometry : angle 0.85446 / 0.38 (15990) hydrogen bonds : bond 0.12921 / 8.64 ( 869) hydrogen bonds : angle 4.94133 / 3.74 ( 2598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.358 Fit side-chains REVERT: B 200 MET cc_start: 0.8008 (ttt) cc_final: 0.7783 (ttm) REVERT: B 231 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8657 (mm-30) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.0872 time to fit residues: 17.1039 Evaluate side-chains 126 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068866 restraints weight = 41705.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070671 restraints weight = 23004.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071779 restraints weight = 16066.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.072540 restraints weight = 12939.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.072919 restraints weight = 11262.229| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11777 Z= 0.169 Angle : 0.627 8.842 15990 Z= 0.317 Chirality : 0.039 0.149 1938 Planarity : 0.004 0.065 1985 Dihedral : 7.413 101.024 1652 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.02 % Allowed : 30.22 % Favored : 65.75 % 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: 2.07 (0.22), residues: 1510 helix: 1.93 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 856 TYR 0.010 0.001 TYR A 594 PHE 0.015 0.001 PHE B 159 TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (11777) covalent geometry : angle 0.62659 / 0.32 (15990) hydrogen bonds : bond 0.04968 / 3.37 ( 869) hydrogen bonds : angle 3.97454 / 3.02 ( 2598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6473 (mmt) REVERT: B 418 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8012 (p) REVERT: B 578 MET cc_start: 0.8879 (ptp) cc_final: 0.8618 (ptt) REVERT: A 113 LEU cc_start: 0.9446 (tp) cc_final: 0.9244 (tt) REVERT: A 154 MET cc_start: 0.8859 (tpp) cc_final: 0.7865 (tpt) REVERT: A 925 MET cc_start: 0.8409 (ppp) cc_final: 0.8200 (tmm) outliers start: 47 outliers final: 18 residues processed: 167 average time/residue: 0.0787 time to fit residues: 20.2572 Evaluate side-chains 140 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 22 optimal weight: 0.0050 chunk 69 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 0.0770 overall best weight: 0.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 GLN A 140 GLN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.095189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072594 restraints weight = 41327.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.074471 restraints weight = 22341.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075659 restraints weight = 15315.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076406 restraints weight = 12141.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076805 restraints weight = 10532.589| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11777 Z= 0.120 Angle : 0.612 11.041 15990 Z= 0.295 Chirality : 0.038 0.133 1938 Planarity : 0.004 0.069 1985 Dihedral : 7.061 92.292 1652 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.08 % Allowed : 30.99 % Favored : 65.92 % 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: 2.37 (0.23), residues: 1510 helix: 2.17 (0.16), residues: 1172 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 605 TYR 0.015 0.001 TYR A 594 PHE 0.012 0.001 PHE A 201 TRP 0.015 0.001 TRP A 643 HIS 0.003 0.000 HIS A 914 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11777) covalent geometry : angle 0.61200 / 0.30 (15990) hydrogen bonds : bond 0.04057 / 2.75 ( 869) hydrogen bonds : angle 3.65784 / 2.80 ( 2598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6574 (mmt) REVERT: B 579 MET cc_start: 0.7382 (mmp) cc_final: 0.7112 (mmm) REVERT: B 586 MET cc_start: 0.8835 (mmm) cc_final: 0.8612 (mmm) REVERT: B 590 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: A 199 MET cc_start: 0.8134 (tpp) cc_final: 0.7771 (mpp) REVERT: A 910 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8375 (ttp80) REVERT: A 925 MET cc_start: 0.8381 (ppp) cc_final: 0.8124 (tmm) outliers start: 36 outliers final: 17 residues processed: 171 average time/residue: 0.0810 time to fit residues: 21.0850 Evaluate side-chains 149 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.0170 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.093804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070851 restraints weight = 41566.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072665 restraints weight = 23034.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073838 restraints weight = 15997.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.074426 restraints weight = 12767.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074946 restraints weight = 11265.557| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11777 Z= 0.124 Angle : 0.614 8.944 15990 Z= 0.299 Chirality : 0.039 0.184 1938 Planarity : 0.004 0.068 1985 Dihedral : 6.815 86.069 1652 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.94 % Allowed : 29.20 % Favored : 66.87 % 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: 2.39 (0.23), residues: 1510 helix: 2.18 (0.16), residues: 1174 sheet: None (None), residues: 0 loop : -0.60 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 605 TYR 0.010 0.001 TYR A 594 PHE 0.022 0.001 PHE A 575 TRP 0.013 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11777) covalent geometry : angle 0.61368 / 0.30 (15990) hydrogen bonds : bond 0.04022 / 2.72 ( 869) hydrogen bonds : angle 3.64524 / 2.78 ( 2598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 401 MET cc_start: 0.8406 (ttt) cc_final: 0.8166 (tmm) REVERT: B 418 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8013 (p) REVERT: B 579 MET cc_start: 0.7499 (mmp) cc_final: 0.7241 (mmm) REVERT: B 586 MET cc_start: 0.8869 (mmm) cc_final: 0.8654 (mmm) REVERT: B 590 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: A 925 MET cc_start: 0.8353 (ppp) cc_final: 0.8078 (tmm) outliers start: 46 outliers final: 25 residues processed: 163 average time/residue: 0.0741 time to fit residues: 18.6703 Evaluate side-chains 149 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 63 optimal weight: 50.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071684 restraints weight = 40874.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073544 restraints weight = 22324.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.074698 restraints weight = 15346.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.075413 restraints weight = 12242.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.075787 restraints weight = 10644.156| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11777 Z= 0.113 Angle : 0.623 13.108 15990 Z= 0.298 Chirality : 0.039 0.164 1938 Planarity : 0.004 0.068 1985 Dihedral : 6.591 79.693 1652 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.68 % Allowed : 30.22 % Favored : 66.10 % 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: 2.45 (0.23), residues: 1510 helix: 2.22 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -0.55 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 605 TYR 0.011 0.001 TYR A 594 PHE 0.012 0.001 PHE A 575 TRP 0.031 0.001 TRP A 643 HIS 0.002 0.000 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11777) covalent geometry : angle 0.62260 / 0.30 (15990) hydrogen bonds : bond 0.03832 / 2.59 ( 869) hydrogen bonds : angle 3.57813 / 2.73 ( 2598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 364 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.9002 (mp) REVERT: B 401 MET cc_start: 0.8593 (ttt) cc_final: 0.8230 (tmm) REVERT: B 418 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7919 (p) REVERT: B 579 MET cc_start: 0.7595 (mmp) cc_final: 0.7272 (mmp) REVERT: B 586 MET cc_start: 0.8902 (mmm) cc_final: 0.8658 (mmm) REVERT: B 590 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: B 613 GLN cc_start: 0.8883 (pp30) cc_final: 0.8659 (pp30) REVERT: A 199 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7771 (mpp) REVERT: A 449 ASP cc_start: 0.7279 (p0) cc_final: 0.6917 (t0) REVERT: A 925 MET cc_start: 0.8432 (ppp) cc_final: 0.8149 (tmm) outliers start: 43 outliers final: 31 residues processed: 169 average time/residue: 0.0834 time to fit residues: 21.5099 Evaluate side-chains 162 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.094738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072054 restraints weight = 41301.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073870 restraints weight = 22804.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075013 restraints weight = 15869.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.075628 restraints weight = 12677.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076128 restraints weight = 11129.334| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11777 Z= 0.111 Angle : 0.626 11.693 15990 Z= 0.298 Chirality : 0.039 0.188 1938 Planarity : 0.004 0.068 1985 Dihedral : 6.370 72.479 1652 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.28 % Allowed : 29.97 % Favored : 65.75 % 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: 2.51 (0.23), residues: 1510 helix: 2.26 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 910 TYR 0.012 0.001 TYR A 594 PHE 0.026 0.001 PHE B 159 TRP 0.023 0.001 TRP A 643 HIS 0.002 0.000 HIS A 914 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11777) covalent geometry : angle 0.62619 / 0.30 (15990) hydrogen bonds : bond 0.03676 / 2.49 ( 869) hydrogen bonds : angle 3.52800 / 2.69 ( 2598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 MET cc_start: 0.8546 (ttt) cc_final: 0.8237 (tmm) REVERT: B 418 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7941 (p) REVERT: B 579 MET cc_start: 0.7524 (mmp) cc_final: 0.7213 (mmp) REVERT: B 586 MET cc_start: 0.8853 (mmm) cc_final: 0.8630 (mmm) REVERT: B 590 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: B 613 GLN cc_start: 0.8851 (pp30) cc_final: 0.8411 (pp30) REVERT: A 199 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: A 449 ASP cc_start: 0.7153 (p0) cc_final: 0.6934 (t0) REVERT: A 925 MET cc_start: 0.8445 (ppp) cc_final: 0.8165 (tmm) outliers start: 50 outliers final: 33 residues processed: 179 average time/residue: 0.0762 time to fit residues: 20.8133 Evaluate side-chains 167 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 21 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 137 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.093978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070549 restraints weight = 41784.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072447 restraints weight = 22430.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073644 restraints weight = 15357.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.074387 restraints weight = 12201.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.074787 restraints weight = 10608.718| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11777 Z= 0.124 Angle : 0.641 12.165 15990 Z= 0.307 Chirality : 0.039 0.200 1938 Planarity : 0.004 0.068 1985 Dihedral : 6.241 66.527 1652 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.94 % Allowed : 29.97 % Favored : 66.10 % 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: 2.48 (0.23), residues: 1510 helix: 2.24 (0.16), residues: 1177 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 910 TYR 0.010 0.001 TYR A 267 PHE 0.039 0.001 PHE A 352 TRP 0.020 0.001 TRP A 643 HIS 0.003 0.000 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11777) covalent geometry : angle 0.64078 / 0.31 (15990) hydrogen bonds : bond 0.03800 / 2.56 ( 869) hydrogen bonds : angle 3.56617 / 2.71 ( 2598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 MET cc_start: 0.8963 (tmm) cc_final: 0.8709 (tmm) REVERT: B 401 MET cc_start: 0.8605 (ttt) cc_final: 0.8299 (tmm) REVERT: B 418 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 579 MET cc_start: 0.7655 (mmp) cc_final: 0.7292 (mmp) REVERT: B 586 MET cc_start: 0.8899 (mmm) cc_final: 0.8654 (mmm) REVERT: B 590 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: B 613 GLN cc_start: 0.8793 (pp30) cc_final: 0.8531 (pp30) REVERT: A 199 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8150 (mpp) REVERT: A 231 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 609 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8244 (ptt90) REVERT: A 925 MET cc_start: 0.8455 (ppp) cc_final: 0.8154 (tmm) outliers start: 46 outliers final: 34 residues processed: 168 average time/residue: 0.0855 time to fit residues: 21.7529 Evaluate side-chains 161 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 82 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.092854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069436 restraints weight = 42164.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071184 restraints weight = 23445.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072301 restraints weight = 16309.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073024 restraints weight = 13107.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.073410 restraints weight = 11463.505| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11777 Z= 0.149 Angle : 0.669 11.637 15990 Z= 0.320 Chirality : 0.039 0.200 1938 Planarity : 0.004 0.068 1985 Dihedral : 6.161 60.051 1652 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.28 % Allowed : 30.05 % Favored : 65.67 % 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: 2.44 (0.22), residues: 1510 helix: 2.22 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 910 TYR 0.010 0.001 TYR A 267 PHE 0.031 0.001 PHE A 352 TRP 0.022 0.001 TRP B 635 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11777) covalent geometry : angle 0.66897 / 0.32 (15990) hydrogen bonds : bond 0.04028 / 2.72 ( 869) hydrogen bonds : angle 3.60982 / 2.73 ( 2598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 231 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8374 (mm-30) REVERT: B 249 MET cc_start: 0.8913 (tmm) cc_final: 0.8664 (tmm) REVERT: B 401 MET cc_start: 0.8561 (ttt) cc_final: 0.8322 (tmm) REVERT: B 418 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 579 MET cc_start: 0.7593 (mmp) cc_final: 0.7244 (mmp) REVERT: B 586 MET cc_start: 0.8879 (mmm) cc_final: 0.8633 (mmm) REVERT: B 590 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: B 613 GLN cc_start: 0.8798 (pp30) cc_final: 0.8543 (pp30) REVERT: A 199 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: A 231 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 609 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8249 (ptt90) outliers start: 50 outliers final: 35 residues processed: 166 average time/residue: 0.0788 time to fit residues: 19.9964 Evaluate side-chains 163 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.093969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070994 restraints weight = 41312.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072823 restraints weight = 22655.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.073970 restraints weight = 15693.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.074702 restraints weight = 12526.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.075096 restraints weight = 10911.175| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11777 Z= 0.118 Angle : 0.669 15.142 15990 Z= 0.314 Chirality : 0.039 0.184 1938 Planarity : 0.004 0.067 1985 Dihedral : 6.021 58.362 1652 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.42 % Allowed : 30.91 % Favored : 65.67 % 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: 2.51 (0.23), residues: 1510 helix: 2.25 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 910 TYR 0.011 0.001 TYR A 594 PHE 0.026 0.001 PHE A 352 TRP 0.023 0.001 TRP B 635 HIS 0.002 0.000 HIS A 914 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11777) covalent geometry : angle 0.66872 / 0.31 (15990) hydrogen bonds : bond 0.03763 / 2.54 ( 869) hydrogen bonds : angle 3.53046 / 2.67 ( 2598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 231 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8319 (mm-30) REVERT: B 249 MET cc_start: 0.8913 (tmm) cc_final: 0.8591 (tmm) REVERT: B 401 MET cc_start: 0.8566 (ttt) cc_final: 0.8310 (tmm) REVERT: B 418 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 579 MET cc_start: 0.7602 (mmp) cc_final: 0.7258 (mmp) REVERT: B 586 MET cc_start: 0.8851 (mmm) cc_final: 0.8608 (mmm) REVERT: B 590 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: B 613 GLN cc_start: 0.8774 (pp30) cc_final: 0.8517 (pp30) REVERT: A 199 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8136 (mpp) REVERT: A 231 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 609 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8206 (ptt90) outliers start: 40 outliers final: 32 residues processed: 159 average time/residue: 0.0866 time to fit residues: 20.8000 Evaluate side-chains 163 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 4 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 145 optimal weight: 0.0980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.094727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072151 restraints weight = 40987.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073934 restraints weight = 22490.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.075125 restraints weight = 15602.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075864 restraints weight = 12364.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.076268 restraints weight = 10709.486| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11777 Z= 0.117 Angle : 0.692 14.551 15990 Z= 0.322 Chirality : 0.039 0.197 1938 Planarity : 0.004 0.067 1985 Dihedral : 5.940 58.361 1652 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.17 % Allowed : 31.16 % Favored : 65.67 % 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: 2.51 (0.23), residues: 1510 helix: 2.25 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 910 TYR 0.011 0.001 TYR A 594 PHE 0.025 0.001 PHE A 352 TRP 0.025 0.001 TRP B 635 HIS 0.002 0.000 HIS A 914 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11777) covalent geometry : angle 0.69224 / 0.32 (15990) hydrogen bonds : bond 0.03644 / 2.47 ( 869) hydrogen bonds : angle 3.50728 / 2.66 ( 2598) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 231 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8447 (mm-30) REVERT: B 249 MET cc_start: 0.8990 (tmm) cc_final: 0.8629 (tmm) REVERT: B 401 MET cc_start: 0.8655 (ttt) cc_final: 0.8334 (tmm) REVERT: B 418 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 579 MET cc_start: 0.7556 (mmp) cc_final: 0.7221 (mmp) REVERT: B 586 MET cc_start: 0.8869 (mmm) cc_final: 0.8655 (mmm) REVERT: B 590 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: B 613 GLN cc_start: 0.8799 (pp30) cc_final: 0.8559 (pp30) REVERT: A 199 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8183 (mpp) REVERT: A 231 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 609 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8164 (ptt90) REVERT: A 925 MET cc_start: 0.8328 (ppp) cc_final: 0.7946 (tmm) outliers start: 37 outliers final: 31 residues processed: 161 average time/residue: 0.0847 time to fit residues: 20.5121 Evaluate side-chains 164 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 63 optimal weight: 40.0000 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.090875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066151 restraints weight = 43356.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068175 restraints weight = 21787.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069479 restraints weight = 14340.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070281 restraints weight = 11105.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070807 restraints weight = 9510.459| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11777 Z= 0.132 Angle : 0.697 14.279 15990 Z= 0.330 Chirality : 0.039 0.205 1938 Planarity : 0.004 0.067 1985 Dihedral : 5.902 58.153 1652 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.17 % Allowed : 31.42 % Favored : 65.41 % 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: 2.50 (0.23), residues: 1510 helix: 2.25 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 910 TYR 0.010 0.001 TYR A 267 PHE 0.024 0.001 PHE A 352 TRP 0.024 0.001 TRP B 635 HIS 0.004 0.000 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11777) covalent geometry : angle 0.69707 / 0.33 (15990) hydrogen bonds : bond 0.03800 / 2.57 ( 869) hydrogen bonds : angle 3.56070 / 2.70 ( 2598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.42 seconds wall clock time: 31 minutes 9.18 seconds (1869.18 seconds total)