Starting phenix.real_space_refine on Sat Aug 23 11:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otw_17185/08_2025/8otw_17185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otw_17185/08_2025/8otw_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 { model { file = "/net/cci-nas-00/data/ceres_data/8otw_17185/08_2025/8otw_17185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otw_17185/08_2025/8otw_17185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8otw_17185/08_2025/8otw_17185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otw_17185/08_2025/8otw_17185.map" } 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-2.0-5787/lib/python3.9/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: 2.74, per 1000 atoms: 0.24 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: 1.02 Conformation dependent library (CDL) restraints added in 358.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.71 Time building geometry restraints manager: 1.29 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 - 35.69: 6805 35.69 - 71.38: 215 71.38 - 107.07: 23 107.07 - 142.75: 2 142.75 - 178.44: 3 Dihedral angle restraints: 7048 sinusoidal: 2638 harmonic: 4410 Sorted by residual: dihedral pdb=" O2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 309.18 130.74 178.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 72.09 -109.78 -178.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C2 CPL A1401 " pdb=" O3P CPL A1401 " ideal model delta sinusoidal sigma weight residual 72.09 -72.57 144.66 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7045 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: 1.860 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 18.411 178.443 4186 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 aren 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 covalent geometry : bond 0.00383 (11777) covalent geometry : angle 0.85446 (15990) hydrogen bonds : bond 0.12921 ( 869) hydrogen bonds : angle 4.94133 ( 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 : 0.302 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: 0.8656 (mm-30) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.0902 time to fit residues: 17.3763 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 : 0.406 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3719 r_free = 0.3719 target = 0.092270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.068902 restraints weight = 41231.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070675 restraints weight = 22804.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071806 restraints weight = 15921.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.072516 restraints weight = 12831.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072907 restraints weight = 11215.103| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0931 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= 0.170 Angle : 0.630 8.736 15990 Z= 0.320 Chirality : 0.039 0.139 1938 Planarity : 0.004 0.065 1985 Dihedral : 10.897 171.165 1672 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.11 % Allowed : 29.97 % 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 aren not related in a simple way. whole: 2.05 (0.22), residues: 1510 helix: 1.92 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.011 0.001 TYR A 594 PHE 0.016 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 covalent geometry : bond 0.00378 (11777) covalent geometry : angle 0.62955 (15990) hydrogen bonds : bond 0.04871 ( 869) hydrogen bonds : angle 3.95920 ( 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: 48 poor density : 127 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6497 (mmt) REVERT: B 418 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8027 (p) REVERT: B 578 MET cc_start: 0.8876 (ptp) cc_final: 0.8608 (ptt) REVERT: A 113 LEU cc_start: 0.9453 (tp) cc_final: 0.9241 (tt) REVERT: A 154 MET cc_start: 0.8894 (tpp) cc_final: 0.7836 (tpt) REVERT: A 587 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8298 (pp) REVERT: A 925 MET cc_start: 0.8406 (ppp) cc_final: 0.8194 (tmm) outliers start: 48 outliers final: 18 residues processed: 167 average time/residue: 0.0916 time to fit residues: 23.6338 Evaluate side-chains 141 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 587 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: 0.9990 chunk 112 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 69 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 GLN A 140 GLN A 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.094606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071936 restraints weight = 40982.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073803 restraints weight = 22128.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074967 restraints weight = 15205.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075719 restraints weight = 12079.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076101 restraints weight = 10467.191| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11777 Z= 0.117 Angle : 0.611 11.107 15990 Z= 0.294 Chirality : 0.038 0.136 1938 Planarity : 0.004 0.069 1985 Dihedral : 10.596 170.289 1672 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.25 % Allowed : 30.99 % 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 aren not related in a simple way. whole: 2.36 (0.23), residues: 1510 helix: 2.16 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 605 TYR 0.016 0.001 TYR A 594 PHE 0.011 0.001 PHE A 201 TRP 0.014 0.001 TRP A 643 HIS 0.002 0.000 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00230 (11777) covalent geometry : angle 0.61092 (15990) hydrogen bonds : bond 0.04128 ( 869) hydrogen bonds : angle 3.66413 ( 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 176 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.438 Fit side-chains REVERT: B 133 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6583 (mmt) REVERT: B 578 MET cc_start: 0.9003 (ptp) cc_final: 0.8771 (ptt) REVERT: B 579 MET cc_start: 0.7412 (mmp) cc_final: 0.7150 (mmm) REVERT: B 586 MET cc_start: 0.8840 (mmm) cc_final: 0.8535 (mmm) REVERT: B 590 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: B 857 MET cc_start: 0.8471 (mmp) cc_final: 0.8174 (mmm) REVERT: A 199 MET cc_start: 0.8145 (tpp) cc_final: 0.7777 (mpp) REVERT: A 910 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8386 (ttp80) REVERT: A 925 MET cc_start: 0.8332 (ppp) cc_final: 0.8074 (tmm) outliers start: 38 outliers final: 20 residues processed: 168 average time/residue: 0.0973 time to fit residues: 24.3951 Evaluate side-chains 150 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 308 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 587 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3731 r_free = 0.3731 target = 0.092916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069893 restraints weight = 41641.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071694 restraints weight = 22960.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072762 restraints weight = 15903.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073357 restraints weight = 12822.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073923 restraints weight = 11352.389| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11777 Z= 0.150 Angle : 0.622 8.692 15990 Z= 0.307 Chirality : 0.039 0.193 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.433 169.019 1672 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.05 % Allowed : 29.11 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.23), residues: 1510 helix: 2.16 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -0.63 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 605 TYR 0.009 0.001 TYR A 594 PHE 0.013 0.001 PHE B 195 TRP 0.013 0.001 TRP A 643 HIS 0.002 0.001 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00337 (11777) covalent geometry : angle 0.62232 (15990) hydrogen bonds : bond 0.04257 ( 869) hydrogen bonds : angle 3.71345 ( 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 187 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: B 418 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 579 MET cc_start: 0.7457 (mmp) cc_final: 0.7199 (mmm) REVERT: B 586 MET cc_start: 0.8865 (mmm) cc_final: 0.8653 (mmm) REVERT: B 590 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: B 857 MET cc_start: 0.8494 (mmp) cc_final: 0.8237 (mmm) REVERT: A 154 MET cc_start: 0.8758 (tpp) cc_final: 0.8367 (tpt) REVERT: A 925 MET cc_start: 0.8383 (ppp) cc_final: 0.8104 (tmm) outliers start: 59 outliers final: 40 residues processed: 175 average time/residue: 0.0939 time to fit residues: 25.4345 Evaluate side-chains 167 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 441 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 B residue 885 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 VAL 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 216 LEU Chi-restraints excluded: chain A residue 229 ILE 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 430 LEU Chi-restraints excluded: chain A residue 587 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 882 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: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 63 optimal weight: 50.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.092518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069236 restraints weight = 42481.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071006 restraints weight = 23390.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072106 restraints weight = 16366.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072803 restraints weight = 13235.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073175 restraints weight = 11608.590| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1409 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= 0.135 Angle : 0.632 14.523 15990 Z= 0.306 Chirality : 0.039 0.177 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.307 168.132 1672 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.62 % Allowed : 28.68 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.23), residues: 1510 helix: 2.19 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -0.62 (0.35), 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 B 598 TRP 0.033 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00298 (11777) covalent geometry : angle 0.63191 (15990) hydrogen bonds : bond 0.04152 ( 869) hydrogen bonds : angle 3.66437 ( 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 185 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.475 Fit side-chains REVERT: B 418 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8006 (p) REVERT: B 579 MET cc_start: 0.7573 (mmp) cc_final: 0.7248 (mmp) REVERT: B 586 MET cc_start: 0.8853 (mmm) cc_final: 0.8626 (mmm) REVERT: B 590 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: A 199 MET cc_start: 0.8321 (tpp) cc_final: 0.8054 (mpp) REVERT: A 449 ASP cc_start: 0.7034 (p0) cc_final: 0.6767 (t0) REVERT: A 911 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 925 MET cc_start: 0.8443 (ppp) cc_final: 0.8158 (tmm) outliers start: 54 outliers final: 38 residues processed: 172 average time/residue: 0.0899 time to fit residues: 23.9079 Evaluate side-chains 164 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU 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 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 B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER 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 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 587 LEU 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 911 GLU 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: 6.9990 chunk 131 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.092809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069342 restraints weight = 42018.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071148 restraints weight = 23327.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072307 restraints weight = 16229.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.073032 restraints weight = 13005.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073396 restraints weight = 11372.019| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11777 Z= 0.131 Angle : 0.635 11.202 15990 Z= 0.308 Chirality : 0.039 0.202 1938 Planarity : 0.004 0.069 1985 Dihedral : 10.226 167.565 1672 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.97 % Allowed : 29.71 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.23), residues: 1510 helix: 2.23 (0.16), residues: 1173 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 605 TYR 0.011 0.001 TYR A 594 PHE 0.013 0.001 PHE A 201 TRP 0.022 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00289 (11777) covalent geometry : angle 0.63454 (15990) hydrogen bonds : bond 0.04086 ( 869) hydrogen bonds : angle 3.63171 ( 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 188 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 130 time to evaluate : 0.568 Fit side-chains REVERT: B 401 MET cc_start: 0.8388 (tpp) cc_final: 0.8117 (tmm) REVERT: B 418 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8002 (p) REVERT: B 579 MET cc_start: 0.7528 (mmp) cc_final: 0.7188 (mmp) REVERT: B 586 MET cc_start: 0.8836 (mmm) cc_final: 0.8602 (mmm) REVERT: B 590 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: A 199 MET cc_start: 0.8338 (tpp) cc_final: 0.7630 (mpp) REVERT: A 588 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9202 (mmmt) REVERT: A 910 ARG cc_start: 0.8610 (tpt90) cc_final: 0.8368 (ttp80) outliers start: 58 outliers final: 43 residues processed: 178 average time/residue: 0.0990 time to fit residues: 27.1947 Evaluate side-chains 169 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 199 MET 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 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 441 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 B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 229 ILE 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 464 VAL Chi-restraints excluded: chain A residue 587 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 21 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 73 optimal weight: 0.0770 chunk 137 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.093810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070593 restraints weight = 41818.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072413 restraints weight = 22815.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073555 restraints weight = 15800.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074145 restraints weight = 12703.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.074623 restraints weight = 11236.353| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11777 Z= 0.116 Angle : 0.641 15.527 15990 Z= 0.305 Chirality : 0.039 0.180 1938 Planarity : 0.004 0.068 1985 Dihedral : 10.135 166.511 1672 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.94 % Allowed : 30.05 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.23), residues: 1510 helix: 2.26 (0.16), residues: 1174 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 605 TYR 0.012 0.001 TYR A 594 PHE 0.013 0.001 PHE A 575 TRP 0.019 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00248 (11777) covalent geometry : angle 0.64090 (15990) hydrogen bonds : bond 0.03828 ( 869) hydrogen bonds : angle 3.54512 ( 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 184 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8515 (pt) cc_final: 0.8258 (pt) REVERT: B 231 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8317 (mm-30) REVERT: B 401 MET cc_start: 0.8450 (tpp) cc_final: 0.8143 (tmm) REVERT: B 418 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 579 MET cc_start: 0.7605 (mmp) cc_final: 0.7265 (mmp) REVERT: B 586 MET cc_start: 0.8839 (mmm) cc_final: 0.8610 (mmm) REVERT: B 590 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: B 613 GLN cc_start: 0.8830 (pp30) cc_final: 0.8368 (pp30) REVERT: A 199 MET cc_start: 0.8411 (tpp) cc_final: 0.7658 (mpp) REVERT: A 231 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: A 587 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8640 (pp) REVERT: A 588 LYS cc_start: 0.9393 (mmmt) cc_final: 0.9184 (mmmt) REVERT: A 925 MET cc_start: 0.8334 (ppp) cc_final: 0.8102 (tmm) outliers start: 46 outliers final: 36 residues processed: 175 average time/residue: 0.0968 time to fit residues: 25.7061 Evaluate side-chains 169 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU 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 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 79 VAL 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 216 LEU Chi-restraints excluded: chain A residue 231 GLU 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 587 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 905 ILE 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: 5.9990 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.093630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070547 restraints weight = 41285.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072364 restraints weight = 22556.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073476 restraints weight = 15608.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.074207 restraints weight = 12506.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.074591 restraints weight = 10906.999| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11777 Z= 0.123 Angle : 0.653 14.050 15990 Z= 0.312 Chirality : 0.039 0.201 1938 Planarity : 0.004 0.068 1985 Dihedral : 10.096 166.070 1672 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.28 % Allowed : 30.31 % 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 aren not related in a simple way. whole: 2.52 (0.23), residues: 1510 helix: 2.26 (0.16), residues: 1174 sheet: None (None), residues: 0 loop : -0.50 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 910 TYR 0.009 0.001 TYR B 312 PHE 0.025 0.001 PHE B 159 TRP 0.019 0.001 TRP A 643 HIS 0.002 0.000 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00272 (11777) covalent geometry : angle 0.65288 (15990) hydrogen bonds : bond 0.03835 ( 869) hydrogen bonds : angle 3.56899 ( 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 177 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8533 (pt) cc_final: 0.8278 (pt) REVERT: B 401 MET cc_start: 0.8452 (tpp) cc_final: 0.8180 (tmm) REVERT: B 418 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8007 (p) REVERT: B 579 MET cc_start: 0.7528 (mmp) cc_final: 0.7203 (mmp) REVERT: B 586 MET cc_start: 0.8796 (mmm) cc_final: 0.8575 (mmm) REVERT: B 590 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: A 199 MET cc_start: 0.8395 (tpp) cc_final: 0.7608 (mpp) REVERT: A 231 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 481 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8588 (mm) outliers start: 50 outliers final: 39 residues processed: 170 average time/residue: 0.0938 time to fit residues: 24.4432 Evaluate side-chains 167 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU 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 424 ILE 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 B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL 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 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 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 464 VAL Chi-restraints excluded: chain A residue 481 LEU 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 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: 2.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 40.0000 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.093382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070089 restraints weight = 41894.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071905 restraints weight = 23205.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072995 restraints weight = 16128.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073746 restraints weight = 13041.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074097 restraints weight = 11367.259| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1714 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= 0.123 Angle : 0.678 13.778 15990 Z= 0.322 Chirality : 0.039 0.198 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.067 165.543 1672 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.77 % Allowed : 31.16 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.22), residues: 1510 helix: 2.24 (0.15), residues: 1173 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 585 TYR 0.010 0.001 TYR A 267 PHE 0.049 0.001 PHE A 352 TRP 0.019 0.001 TRP A 643 HIS 0.002 0.000 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00272 (11777) covalent geometry : angle 0.67755 (15990) hydrogen bonds : bond 0.03799 ( 869) hydrogen bonds : angle 3.56539 ( 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 175 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.455 Fit side-chains REVERT: B 81 ILE cc_start: 0.8563 (pt) cc_final: 0.8297 (pt) REVERT: B 401 MET cc_start: 0.8476 (tpp) cc_final: 0.8184 (tmm) REVERT: B 418 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7990 (p) REVERT: B 579 MET cc_start: 0.7560 (mmp) cc_final: 0.7229 (mmp) REVERT: B 586 MET cc_start: 0.8816 (mmm) cc_final: 0.8615 (mmm) REVERT: B 590 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: B 613 GLN cc_start: 0.8750 (pp30) cc_final: 0.8479 (pp30) REVERT: A 199 MET cc_start: 0.8442 (tpp) cc_final: 0.7633 (mpp) REVERT: A 205 MET cc_start: 0.8511 (tpp) cc_final: 0.8259 (mtp) REVERT: A 231 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 481 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8605 (mm) outliers start: 44 outliers final: 37 residues processed: 168 average time/residue: 0.0992 time to fit residues: 25.4131 Evaluate side-chains 169 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU 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 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 B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL 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 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 481 LEU 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 905 ILE 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: 4.9990 chunk 94 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.091265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066610 restraints weight = 42652.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.068649 restraints weight = 21456.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069940 restraints weight = 14078.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070780 restraints weight = 10911.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071164 restraints weight = 9300.639| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11777 Z= 0.121 Angle : 0.688 13.632 15990 Z= 0.326 Chirality : 0.039 0.200 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.049 164.896 1672 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.85 % Allowed : 30.99 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.23), residues: 1510 helix: 2.22 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 910 TYR 0.010 0.001 TYR A 594 PHE 0.047 0.001 PHE A 352 TRP 0.019 0.001 TRP B 635 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00265 (11777) covalent geometry : angle 0.68758 (15990) hydrogen bonds : bond 0.03765 ( 869) hydrogen bonds : angle 3.56791 ( 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 175 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 367 MET cc_start: 0.7838 (mtm) cc_final: 0.7635 (mtm) REVERT: B 401 MET cc_start: 0.8808 (tpp) cc_final: 0.8320 (tmm) REVERT: B 418 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7647 (p) REVERT: B 579 MET cc_start: 0.8008 (mmp) cc_final: 0.7561 (mmp) REVERT: B 586 MET cc_start: 0.9004 (mmm) cc_final: 0.8735 (mmm) REVERT: B 590 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: B 613 GLN cc_start: 0.8953 (pp30) cc_final: 0.8682 (pp30) REVERT: A 199 MET cc_start: 0.8887 (tpp) cc_final: 0.7763 (mpp) REVERT: A 231 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 481 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8635 (mm) outliers start: 45 outliers final: 38 residues processed: 166 average time/residue: 0.1008 time to fit residues: 25.2520 Evaluate side-chains 167 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU 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 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 B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL 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 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 481 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 905 ILE 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 26 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 63 optimal weight: 50.0000 chunk 137 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 127 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.091589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066891 restraints weight = 43050.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068911 restraints weight = 21676.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.070178 restraints weight = 14212.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071017 restraints weight = 11035.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071407 restraints weight = 9395.802| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1856 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= 0.122 Angle : 0.710 13.595 15990 Z= 0.335 Chirality : 0.040 0.197 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.023 164.395 1672 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.51 % Allowed : 32.11 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.23), residues: 1510 helix: 2.21 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 910 TYR 0.011 0.001 TYR A 594 PHE 0.043 0.001 PHE A 352 TRP 0.019 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00267 (11777) covalent geometry : angle 0.71040 (15990) hydrogen bonds : bond 0.03704 ( 869) hydrogen bonds : angle 3.55053 ( 2598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.47 seconds wall clock time: 37 minutes 27.35 seconds (2247.35 seconds total)