Starting phenix.real_space_refine on Wed Jul 30 02:30:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otw_17185/07_2025/8otw_17185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otw_17185/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2025/8otw_17185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2025/8otw_17185.map" model { file = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2025/8otw_17185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otw_17185/07_2025/8otw_17185.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} 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: 7.31, per 1000 atoms: 0.63 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.10 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: 3.53 Time building geometry restraints manager: 3.54 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- 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 : 13.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.001 TRP A 643 HIS 0.004 0.001 HIS A 502 PHE 0.042 0.001 PHE A 352 TYR 0.010 0.001 TYR B 387 ARG 0.005 0.000 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.12921 ( 869) hydrogen bonds : angle 4.94133 ( 2598) covalent geometry : bond 0.00383 (11777) covalent geometry : angle 0.85446 (15990) *********************** 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 : 1.289 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: 0.2201 time to fit residues: 42.6455 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 : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 50.0000 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 137 optimal weight: 10.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.092365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069167 restraints weight = 40885.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070931 restraints weight = 22660.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072035 restraints weight = 15857.656| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11777 Z= 0.187 Angle : 0.640 9.077 15990 Z= 0.325 Chirality : 0.039 0.152 1938 Planarity : 0.004 0.064 1985 Dihedral : 10.964 171.604 1672 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.60 % Allowed : 30.91 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.22), residues: 1510 helix: 1.92 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.67 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS B 157 PHE 0.017 0.001 PHE B 159 TYR 0.011 0.001 TYR A 594 ARG 0.007 0.000 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 869) hydrogen bonds : angle 4.04559 ( 2598) covalent geometry : bond 0.00418 (11777) covalent geometry : angle 0.64049 (15990) *********************** 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 169 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6631 (mmt) REVERT: B 401 MET cc_start: 0.8581 (ttt) cc_final: 0.8343 (tmm) REVERT: B 578 MET cc_start: 0.8902 (ptp) cc_final: 0.8654 (ptt) REVERT: A 154 MET cc_start: 0.8967 (tpp) cc_final: 0.7970 (tpt) REVERT: A 925 MET cc_start: 0.8477 (ppp) cc_final: 0.8273 (tmm) outliers start: 42 outliers final: 18 residues processed: 162 average time/residue: 0.2025 time to fit residues: 50.1871 Evaluate side-chains 139 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 441 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.094025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071271 restraints weight = 40864.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073107 restraints weight = 22176.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.074287 restraints weight = 15263.755| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11777 Z= 0.118 Angle : 0.608 10.644 15990 Z= 0.296 Chirality : 0.039 0.141 1938 Planarity : 0.004 0.069 1985 Dihedral : 10.659 170.600 1672 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.68 % Allowed : 30.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.23), residues: 1510 helix: 2.13 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -0.60 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 643 HIS 0.003 0.000 HIS A 914 PHE 0.012 0.001 PHE A 201 TYR 0.013 0.001 TYR A 594 ARG 0.003 0.000 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 869) hydrogen bonds : angle 3.72130 ( 2598) covalent geometry : bond 0.00242 (11777) covalent geometry : angle 0.60755 (15990) *********************** 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 177 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6676 (mmt) REVERT: B 401 MET cc_start: 0.8635 (ttt) cc_final: 0.8331 (tmm) REVERT: B 418 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 579 MET cc_start: 0.7498 (mmp) cc_final: 0.7242 (mmm) REVERT: B 586 MET cc_start: 0.8883 (mmm) cc_final: 0.8661 (mmm) REVERT: B 590 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: A 910 ARG cc_start: 0.8630 (tpt90) cc_final: 0.8374 (ttp80) REVERT: A 925 MET cc_start: 0.8386 (ppp) cc_final: 0.8131 (tmm) outliers start: 43 outliers final: 21 residues processed: 167 average time/residue: 0.2034 time to fit residues: 51.2321 Evaluate side-chains 146 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE 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 308 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 862 LYS 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 72 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 121 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** A 614 HIS A 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.094746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072009 restraints weight = 40967.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073866 restraints weight = 22440.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.074932 restraints weight = 15456.872| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11777 Z= 0.113 Angle : 0.604 9.710 15990 Z= 0.292 Chirality : 0.038 0.177 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.444 169.096 1672 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.54 % Allowed : 29.37 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.23), residues: 1510 helix: 2.20 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 PHE 0.010 0.001 PHE A 87 TYR 0.012 0.001 TYR A 594 ARG 0.003 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 869) hydrogen bonds : angle 3.60100 ( 2598) covalent geometry : bond 0.00228 (11777) covalent geometry : angle 0.60388 (15990) *********************** 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 189 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: B 401 MET cc_start: 0.8631 (ttt) cc_final: 0.8220 (tmm) REVERT: B 418 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 473 THR cc_start: 0.8705 (m) cc_final: 0.8496 (m) REVERT: B 579 MET cc_start: 0.7716 (mmp) cc_final: 0.7384 (mmm) REVERT: B 586 MET cc_start: 0.8953 (mmm) cc_final: 0.8707 (mmm) REVERT: B 590 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: B 857 MET cc_start: 0.8293 (mmp) cc_final: 0.8022 (mmm) REVERT: A 199 MET cc_start: 0.8241 (tpp) cc_final: 0.7750 (mpp) REVERT: A 925 MET cc_start: 0.8417 (ppp) cc_final: 0.8133 (tmm) outliers start: 53 outliers final: 27 residues processed: 179 average time/residue: 0.2204 time to fit residues: 59.9608 Evaluate side-chains 156 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 266 LEU 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 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.094319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071220 restraints weight = 40866.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.073048 restraints weight = 22488.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.074150 restraints weight = 15616.095| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11777 Z= 0.116 Angle : 0.633 13.512 15990 Z= 0.303 Chirality : 0.039 0.190 1938 Planarity : 0.004 0.068 1985 Dihedral : 10.313 168.234 1672 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.51 % Allowed : 30.39 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.23), residues: 1510 helix: 2.21 (0.16), residues: 1178 sheet: None (None), residues: 0 loop : -0.54 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 643 HIS 0.003 0.000 HIS A 614 PHE 0.011 0.001 PHE A 201 TYR 0.012 0.001 TYR A 594 ARG 0.003 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 869) hydrogen bonds : angle 3.59104 ( 2598) covalent geometry : bond 0.00248 (11777) covalent geometry : angle 0.63272 (15990) *********************** 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 171 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: B 249 MET cc_start: 0.8960 (tmm) cc_final: 0.8711 (tmm) REVERT: B 401 MET cc_start: 0.8661 (ttt) cc_final: 0.8219 (tmm) REVERT: B 418 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7939 (p) REVERT: B 473 THR cc_start: 0.8654 (m) cc_final: 0.8450 (m) REVERT: B 579 MET cc_start: 0.7715 (mmp) cc_final: 0.7362 (mmp) REVERT: B 586 MET cc_start: 0.8930 (mmm) cc_final: 0.8676 (mmm) REVERT: B 590 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: B 613 GLN cc_start: 0.8918 (pp30) cc_final: 0.8696 (pp30) REVERT: B 857 MET cc_start: 0.8382 (mmp) cc_final: 0.8179 (mmm) REVERT: A 199 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7754 (mpp) REVERT: A 449 ASP cc_start: 0.7310 (p0) cc_final: 0.6951 (t0) REVERT: A 925 MET cc_start: 0.8444 (ppp) cc_final: 0.8154 (tmm) outliers start: 41 outliers final: 31 residues processed: 161 average time/residue: 0.2137 time to fit residues: 52.0464 Evaluate side-chains 160 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 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 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 117 optimal weight: 0.0570 chunk 3 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.095270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072270 restraints weight = 41969.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.074114 restraints weight = 22863.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075297 restraints weight = 15807.490| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11777 Z= 0.112 Angle : 0.631 11.498 15990 Z= 0.300 Chirality : 0.039 0.167 1938 Planarity : 0.004 0.068 1985 Dihedral : 10.175 167.279 1672 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.11 % Allowed : 29.28 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.23), residues: 1510 helix: 2.26 (0.16), residues: 1178 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 643 HIS 0.002 0.000 HIS A 914 PHE 0.026 0.001 PHE B 159 TYR 0.013 0.001 TYR A 594 ARG 0.004 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 869) hydrogen bonds : angle 3.51562 ( 2598) covalent geometry : bond 0.00232 (11777) covalent geometry : angle 0.63091 (15990) *********************** 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 190 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 2.444 Fit side-chains REVERT: B 231 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8451 (mm-30) REVERT: B 249 MET cc_start: 0.8911 (tmm) cc_final: 0.8575 (tmm) REVERT: B 401 MET cc_start: 0.8648 (ttt) cc_final: 0.8232 (tmm) REVERT: B 418 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7926 (p) REVERT: B 579 MET cc_start: 0.7605 (mmp) cc_final: 0.7263 (mmp) REVERT: B 586 MET cc_start: 0.8864 (mmm) cc_final: 0.8630 (mmm) REVERT: B 590 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: B 613 GLN cc_start: 0.8874 (pp30) cc_final: 0.8444 (pp30) REVERT: A 199 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7743 (mpp) REVERT: A 449 ASP cc_start: 0.7248 (p0) cc_final: 0.7017 (t0) outliers start: 48 outliers final: 30 residues processed: 179 average time/residue: 0.2429 time to fit residues: 65.8320 Evaluate side-chains 164 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 GLN A 614 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072387 restraints weight = 41948.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.074288 restraints weight = 22927.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075464 restraints weight = 15790.809| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11777 Z= 0.113 Angle : 0.649 12.088 15990 Z= 0.308 Chirality : 0.039 0.192 1938 Planarity : 0.004 0.068 1985 Dihedral : 10.110 166.724 1672 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.02 % Allowed : 29.71 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.22), residues: 1510 helix: 2.28 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.002 0.000 HIS A 914 PHE 0.014 0.001 PHE A 201 TYR 0.012 0.001 TYR A 594 ARG 0.004 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 869) hydrogen bonds : angle 3.52096 ( 2598) covalent geometry : bond 0.00237 (11777) covalent geometry : angle 0.64883 (15990) *********************** 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: 47 poor density : 137 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: B 249 MET cc_start: 0.8901 (tmm) cc_final: 0.8565 (tmm) REVERT: B 401 MET cc_start: 0.8665 (ttt) cc_final: 0.8251 (tmm) REVERT: B 418 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 579 MET cc_start: 0.7613 (mmp) cc_final: 0.7274 (mmp) REVERT: B 586 MET cc_start: 0.8867 (mmm) cc_final: 0.8651 (mmm) REVERT: B 590 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: A 199 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7781 (mpp) REVERT: A 231 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 448 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7758 (p0) REVERT: A 588 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9243 (mmmt) REVERT: A 838 ASP cc_start: 0.8692 (m-30) cc_final: 0.8456 (m-30) outliers start: 47 outliers final: 30 residues processed: 174 average time/residue: 0.2115 time to fit residues: 55.4577 Evaluate side-chains 163 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 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 448 ASN 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 882 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 96 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 chunk 136 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.095645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072776 restraints weight = 41413.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.074642 restraints weight = 22583.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.075834 restraints weight = 15571.087| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11777 Z= 0.113 Angle : 0.656 12.188 15990 Z= 0.311 Chirality : 0.039 0.191 1938 Planarity : 0.004 0.068 1985 Dihedral : 10.036 166.145 1672 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.60 % Allowed : 30.22 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.23), residues: 1510 helix: 2.26 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.44 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.000 HIS B 614 PHE 0.034 0.001 PHE B 352 TYR 0.009 0.001 TYR B 312 ARG 0.004 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 869) hydrogen bonds : angle 3.50503 ( 2598) covalent geometry : bond 0.00241 (11777) covalent geometry : angle 0.65605 (15990) *********************** 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: 42 poor density : 135 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: B 231 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 249 MET cc_start: 0.8925 (tmm) cc_final: 0.8577 (tmm) REVERT: B 401 MET cc_start: 0.8685 (ttt) cc_final: 0.8242 (tmm) REVERT: B 418 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 579 MET cc_start: 0.7636 (mmp) cc_final: 0.7207 (mmp) REVERT: B 586 MET cc_start: 0.8877 (mmm) cc_final: 0.8659 (mmm) REVERT: B 590 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: A 154 MET cc_start: 0.8959 (tpp) cc_final: 0.8469 (tpt) REVERT: A 199 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7717 (mpp) REVERT: A 231 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7746 (mp0) outliers start: 42 outliers final: 30 residues processed: 166 average time/residue: 0.2134 time to fit residues: 53.5236 Evaluate side-chains 163 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 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 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 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.092499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068748 restraints weight = 42379.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070573 restraints weight = 22888.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071749 restraints weight = 15834.352| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11777 Z= 0.163 Angle : 0.698 13.242 15990 Z= 0.337 Chirality : 0.040 0.214 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.074 166.243 1672 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.25 % Allowed : 30.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.22), residues: 1510 helix: 2.20 (0.16), residues: 1177 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 PHE 0.029 0.002 PHE A 148 TYR 0.011 0.001 TYR A 267 ARG 0.008 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 869) hydrogen bonds : angle 3.63615 ( 2598) covalent geometry : bond 0.00369 (11777) covalent geometry : angle 0.69840 (15990) *********************** 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 162 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: B 249 MET cc_start: 0.9012 (tmm) cc_final: 0.8669 (tmm) REVERT: B 401 MET cc_start: 0.8777 (ttt) cc_final: 0.8387 (tmm) REVERT: B 418 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 579 MET cc_start: 0.7823 (mmp) cc_final: 0.7414 (mmp) REVERT: B 586 MET cc_start: 0.8920 (mmm) cc_final: 0.8652 (mmm) REVERT: B 590 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: A 199 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8153 (mpp) REVERT: A 231 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 911 GLU cc_start: 0.8509 (mp0) cc_final: 0.8304 (pm20) outliers start: 38 outliers final: 29 residues processed: 156 average time/residue: 0.2114 time to fit residues: 49.9956 Evaluate side-chains 157 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 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 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 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 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.092149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067412 restraints weight = 42669.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.069458 restraints weight = 21499.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070756 restraints weight = 14132.033| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11777 Z= 0.119 Angle : 0.710 18.163 15990 Z= 0.330 Chirality : 0.039 0.188 1938 Planarity : 0.004 0.066 1985 Dihedral : 10.011 165.198 1672 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.57 % Allowed : 31.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.23), residues: 1510 helix: 2.27 (0.16), residues: 1179 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 635 HIS 0.002 0.000 HIS B 157 PHE 0.027 0.001 PHE B 352 TYR 0.011 0.001 TYR A 594 ARG 0.008 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 869) hydrogen bonds : angle 3.49378 ( 2598) covalent geometry : bond 0.00256 (11777) covalent geometry : angle 0.71011 (15990) ********************** 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 162 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: B 249 MET cc_start: 0.9294 (tmm) cc_final: 0.8965 (tmm) REVERT: B 401 MET cc_start: 0.9047 (ttt) cc_final: 0.8420 (tmm) REVERT: B 418 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 579 MET cc_start: 0.8093 (mmp) cc_final: 0.7634 (mmp) REVERT: B 586 MET cc_start: 0.9038 (mmm) cc_final: 0.8776 (mmm) REVERT: B 590 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: A 199 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8299 (mpp) REVERT: A 231 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: A 249 MET cc_start: 0.8833 (ttp) cc_final: 0.8351 (tmm) REVERT: A 838 ASP cc_start: 0.8620 (m-30) cc_final: 0.8185 (m-30) REVERT: A 925 MET cc_start: 0.8567 (ppp) cc_final: 0.8354 (tmm) outliers start: 30 outliers final: 25 residues processed: 153 average time/residue: 0.2088 time to fit residues: 48.1390 Evaluate side-chains 155 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 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 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.090957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.066240 restraints weight = 43091.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068214 restraints weight = 21737.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069536 restraints weight = 14416.454| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11777 Z= 0.143 Angle : 0.727 15.298 15990 Z= 0.344 Chirality : 0.040 0.205 1938 Planarity : 0.004 0.067 1985 Dihedral : 10.015 165.152 1672 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.74 % Allowed : 31.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.22), residues: 1510 helix: 2.29 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 635 HIS 0.002 0.000 HIS B 600 PHE 0.025 0.001 PHE B 352 TYR 0.010 0.001 TYR A 267 ARG 0.008 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 869) hydrogen bonds : angle 3.56695 ( 2598) covalent geometry : bond 0.00329 (11777) covalent geometry : angle 0.72650 (15990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3858.32 seconds wall clock time: 69 minutes 3.59 seconds (4143.59 seconds total)