Starting phenix.real_space_refine on Fri Jul 3 16:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5c_29739/07_2026/8g5c_29739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5c_29739/07_2026/8g5c_29739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g5c_29739/07_2026/8g5c_29739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5c_29739/07_2026/8g5c_29739_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5c_29739/07_2026/8g5c_29739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5c_29739/07_2026/8g5c_29739.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.182 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 18 5.49 5 S 106 5.16 5 C 9426 2.51 5 N 2504 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14873 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1032, 7981 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 982} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1032, 7981 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 982} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 8143 Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 153 Unusual residues: {'ADP': 1, 'COA': 1, 'FLC': 1, 'PO4': 1, 'Q5B': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'COA': 1, 'FLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'COA': 1, 'FLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'COA': 1, 'FLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 3.92, per 1000 atoms: 0.26 Number of scatterers: 14873 At special positions: 0 Unit cell: (132.8, 113.71, 131.97, 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 106 16.00 P 18 15.00 O 2819 8.00 N 2504 7.00 C 9426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 726.7 milliseconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 19 sheets defined 55.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.591A pdb=" N LYS A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.579A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 6.601A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.682A pdb=" N ASP A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.642A pdb=" N ARG A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 364 removed outlier: 4.065A pdb=" N GLY A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.611A pdb=" N LEU A 368 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 412 through 419 removed outlier: 3.743A pdb=" N GLY A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.654A pdb=" N ALA A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 587 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.638A pdb=" N HIS A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 733 Processing helix chain 'A' and resid 746 through 750 removed outlier: 3.917A pdb=" N THR A 750 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 792 through 807 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 937 through 952 Processing helix chain 'A' and resid 955 through 966 Processing helix chain 'A' and resid 984 through 998 Processing helix chain 'A' and resid 1001 through 1018 Processing helix chain 'A' and resid 1024 through 1040 Processing helix chain 'A' and resid 1044 through 1055 Processing helix chain 'A' and resid 1055 through 1080 removed outlier: 3.857A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 867 through 879 Processing helix chain 'B' and resid 883 through 897 Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 937 through 952 Processing helix chain 'B' and resid 955 through 967 Processing helix chain 'B' and resid 984 through 998 Processing helix chain 'B' and resid 1001 through 1016 Processing helix chain 'B' and resid 1024 through 1040 Processing helix chain 'B' and resid 1044 through 1055 Processing helix chain 'B' and resid 1055 through 1080 removed outlier: 3.809A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'C' and resid 825 through 832 Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 879 Processing helix chain 'C' and resid 883 through 897 Processing helix chain 'C' and resid 904 through 916 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 937 through 952 Processing helix chain 'C' and resid 955 through 966 Processing helix chain 'C' and resid 984 through 998 Processing helix chain 'C' and resid 1001 through 1018 Processing helix chain 'C' and resid 1024 through 1040 Processing helix chain 'C' and resid 1044 through 1055 removed outlier: 3.525A pdb=" N GLY C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1079 removed outlier: 3.823A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1089 No H-bonds generated for 'chain 'C' and resid 1087 through 1089' Processing helix chain 'D' and resid 825 through 832 Processing helix chain 'D' and resid 859 through 865 Processing helix chain 'D' and resid 868 through 879 Processing helix chain 'D' and resid 883 through 897 Processing helix chain 'D' and resid 904 through 916 Processing helix chain 'D' and resid 919 through 929 Processing helix chain 'D' and resid 937 through 952 Processing helix chain 'D' and resid 955 through 966 Processing helix chain 'D' and resid 984 through 998 Processing helix chain 'D' and resid 1001 through 1017 Processing helix chain 'D' and resid 1024 through 1040 Processing helix chain 'D' and resid 1044 through 1055 removed outlier: 3.516A pdb=" N GLY D1055 " --> pdb=" O TYR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1079 removed outlier: 3.844A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1089 No H-bonds generated for 'chain 'D' and resid 1087 through 1089' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.580A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE A 119 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.580A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.770A pdb=" N VAL A 57 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL A 74 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 268 Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.720A pdb=" N LYS A 336 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE A 376 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ARG A 378 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 340 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 543 removed outlier: 7.144A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 498 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 635 removed outlier: 6.928A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 713 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TRP A 743 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 715 " --> pdb=" O TRP A 743 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 745 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A 717 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 823 through 824 removed outlier: 6.420A pdb=" N MET A 823 " --> pdb=" O ARG B 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 834 through 835 Processing sheet with id=AB1, first strand: chain 'A' and resid 840 through 842 removed outlier: 6.793A pdb=" N PHE A 840 " --> pdb=" O SER D1092 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 845 through 846 Processing sheet with id=AB3, first strand: chain 'A' and resid 1091 through 1093 Processing sheet with id=AB4, first strand: chain 'B' and resid 840 through 842 removed outlier: 6.663A pdb=" N PHE B 840 " --> pdb=" O SER C1092 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 845 through 846 Processing sheet with id=AB6, first strand: chain 'B' and resid 1091 through 1093 Processing sheet with id=AB7, first strand: chain 'C' and resid 823 through 824 removed outlier: 6.741A pdb=" N MET C 823 " --> pdb=" O ARG D 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 834 through 835 Processing sheet with id=AB9, first strand: chain 'C' and resid 845 through 846 Processing sheet with id=AC1, first strand: chain 'D' and resid 845 through 846 789 hydrogen bonds defined for protein. 2304 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: 2.48 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2424 1.31 - 1.45: 3944 1.45 - 1.58: 8558 1.58 - 1.72: 31 1.72 - 1.86: 176 Bond restraints: 15133 Sorted by residual: bond pdb=" C5 Q5B A1205 " pdb=" C6 Q5B A1205 " ideal model delta sigma weight residual 1.539 1.313 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C18 Q5B A1205 " pdb=" N6 Q5B A1205 " ideal model delta sigma weight residual 1.337 1.490 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C5 Q5B A1205 " pdb=" O7 Q5B A1205 " ideal model delta sigma weight residual 1.437 1.578 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C8 Q5B A1205 " pdb=" O7 Q5B A1205 " ideal model delta sigma weight residual 1.391 1.504 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" O12 Q5B A1205 " pdb=" P2 Q5B A1205 " ideal model delta sigma weight residual 1.525 1.420 0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 15128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 20222 3.26 - 6.51: 225 6.51 - 9.77: 39 9.77 - 13.03: 12 13.03 - 16.28: 3 Bond angle restraints: 20501 Sorted by residual: angle pdb=" C11 Q5B A1205 " pdb=" N Q5B A1205 " pdb=" C8 Q5B A1205 " ideal model delta sigma weight residual 126.56 110.28 16.28 3.00e+00 1.11e-01 2.95e+01 angle pdb=" N LYS B1017 " pdb=" CA LYS B1017 " pdb=" C LYS B1017 " ideal model delta sigma weight residual 110.80 99.46 11.34 2.13e+00 2.20e-01 2.84e+01 angle pdb=" CA PRO D1019 " pdb=" N PRO D1019 " pdb=" CD PRO D1019 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.77e+01 angle pdb=" P1A COA D2101 " pdb=" O3A COA D2101 " pdb=" P2A COA D2101 " ideal model delta sigma weight residual 135.11 120.15 14.96 3.00e+00 1.11e-01 2.49e+01 angle pdb=" O1 Q5B A1205 " pdb=" P Q5B A1205 " pdb=" O2 Q5B A1205 " ideal model delta sigma weight residual 120.25 106.45 13.80 3.00e+00 1.11e-01 2.12e+01 ... (remaining 20496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.54: 8656 31.54 - 63.07: 444 63.07 - 94.61: 36 94.61 - 126.15: 0 126.15 - 157.68: 2 Dihedral angle restraints: 9138 sinusoidal: 3822 harmonic: 5316 Sorted by residual: dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 97.68 -157.68 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C4 Q5B A1205 " pdb=" O6 Q5B A1205 " pdb=" P1 Q5B A1205 " pdb=" O5 Q5B A1205 " ideal model delta sinusoidal sigma weight residual 42.71 -161.81 -155.48 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CA ILE A 621 " pdb=" C ILE A 621 " pdb=" N GLY A 622 " pdb=" CA GLY A 622 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 9135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2018 0.069 - 0.138: 218 0.138 - 0.207: 12 0.207 - 0.276: 3 0.276 - 0.345: 1 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C7 Q5B A1205 " pdb=" C6 Q5B A1205 " pdb=" C8 Q5B A1205 " pdb=" O8 Q5B A1205 " both_signs ideal model delta sigma weight residual False 2.49 2.84 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C23 Q5B A1205 " pdb=" C22 Q5B A1205 " pdb=" C26 Q5B A1205 " pdb=" O20 Q5B A1205 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C3B COA C2101 " pdb=" C2B COA C2101 " pdb=" C4B COA C2101 " pdb=" O3B COA C2101 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2249 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P COA D2101 " 0.224 2.00e-02 2.50e+03 1.87e-01 4.37e+02 pdb=" C5P COA D2101 " -0.060 2.00e-02 2.50e+03 pdb=" C6P COA D2101 " 0.157 2.00e-02 2.50e+03 pdb=" N4P COA D2101 " -0.310 2.00e-02 2.50e+03 pdb=" O5P COA D2101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA C2101 " -0.137 2.00e-02 2.50e+03 1.13e-01 1.58e+02 pdb=" C9P COA C2101 " 0.035 2.00e-02 2.50e+03 pdb=" CAP COA C2101 " -0.101 2.00e-02 2.50e+03 pdb=" N8P COA C2101 " 0.181 2.00e-02 2.50e+03 pdb=" O9P COA C2101 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA D2101 " 0.134 2.00e-02 2.50e+03 1.09e-01 1.49e+02 pdb=" C9P COA D2101 " -0.038 2.00e-02 2.50e+03 pdb=" CAP COA D2101 " 0.101 2.00e-02 2.50e+03 pdb=" N8P COA D2101 " -0.172 2.00e-02 2.50e+03 pdb=" O9P COA D2101 " -0.025 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3350 2.79 - 3.31: 14520 3.31 - 3.84: 27241 3.84 - 4.37: 32504 4.37 - 4.90: 53429 Nonbonded interactions: 131044 Sorted by model distance: nonbonded pdb=" OH TYR A 725 " pdb=" O SER A 769 " model vdw 2.257 3.040 nonbonded pdb=" OE2 GLU D 851 " pdb=" OG1 THR D 860 " model vdw 2.286 3.040 nonbonded pdb=" OD2 ASP A 516 " pdb=" OG SER A 525 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 625 " pdb=" O ALA A 686 " model vdw 2.294 3.040 nonbonded pdb=" O ALA C 943 " pdb=" OG SER C 947 " model vdw 2.295 3.040 ... (remaining 131039 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 13.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.006 0.226 15133 Z= 0.285 Angle : 0.842 16.283 20501 Z= 0.354 Chirality : 0.044 0.345 2252 Planarity : 0.007 0.187 2589 Dihedral : 17.514 157.681 5756 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.04 % Allowed : 22.61 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1859 helix: 1.69 (0.16), residues: 1000 sheet: 0.59 (0.47), residues: 133 loop : -0.04 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1085 TYR 0.030 0.002 TYR A 304 PHE 0.011 0.001 PHE A 752 TRP 0.020 0.001 TRP D 827 HIS 0.003 0.001 HIS A 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.29 (15133) covalent geometry : angle 0.84199 / 0.35 (20501) hydrogen bonds : bond 0.11657 / 7.82 ( 782) hydrogen bonds : angle 5.56439 / 3.81 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 0.427 Fit side-chains REVERT: A 30 LYS cc_start: 0.6330 (mttm) cc_final: 0.5296 (tmtt) REVERT: A 61 GLN cc_start: 0.7085 (mt0) cc_final: 0.6696 (mt0) REVERT: A 158 GLU cc_start: 0.6472 (pt0) cc_final: 0.6143 (pt0) REVERT: A 199 TYR cc_start: 0.7787 (t80) cc_final: 0.7560 (t80) REVERT: A 204 PRO cc_start: 0.7104 (Cg_endo) cc_final: 0.6571 (Cg_exo) REVERT: A 205 LEU cc_start: 0.5181 (tp) cc_final: 0.4870 (tp) REVERT: A 256 LEU cc_start: 0.7168 (mt) cc_final: 0.6575 (mt) REVERT: A 294 ASP cc_start: 0.7071 (t70) cc_final: 0.6800 (t0) REVERT: A 385 GLN cc_start: 0.7204 (pm20) cc_final: 0.6827 (pm20) REVERT: A 751 MET cc_start: 0.5386 (ppp) cc_final: 0.5113 (pmm) REVERT: A 791 ASP cc_start: 0.7073 (m-30) cc_final: 0.6853 (m-30) REVERT: A 865 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 1024 ASN cc_start: 0.7482 (m110) cc_final: 0.7191 (m-40) REVERT: A 1089 ASP cc_start: 0.7690 (p0) cc_final: 0.7401 (p0) REVERT: B 826 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7979 (p) REVERT: B 988 GLN cc_start: 0.7594 (tp40) cc_final: 0.7096 (mm110) REVERT: B 1067 MET cc_start: 0.7773 (mtp) cc_final: 0.7469 (mtm) REVERT: C 857 MET cc_start: 0.8705 (ttm) cc_final: 0.8254 (mtp) REVERT: C 864 LYS cc_start: 0.8257 (ttmt) cc_final: 0.8048 (mttm) REVERT: C 940 ASP cc_start: 0.7920 (t70) cc_final: 0.7618 (t70) REVERT: C 992 ASP cc_start: 0.7877 (m-30) cc_final: 0.7607 (m-30) REVERT: C 1067 MET cc_start: 0.7518 (ttm) cc_final: 0.7254 (mtm) REVERT: C 1089 ASP cc_start: 0.7847 (p0) cc_final: 0.7555 (p0) REVERT: D 857 MET cc_start: 0.8775 (ttm) cc_final: 0.8541 (ttp) REVERT: D 881 ARG cc_start: 0.7624 (tpt-90) cc_final: 0.7384 (tpt-90) REVERT: D 940 ASP cc_start: 0.7946 (t70) cc_final: 0.7673 (t70) REVERT: D 1078 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7470 (ttp-110) REVERT: D 1089 ASP cc_start: 0.7714 (p0) cc_final: 0.7416 (p0) outliers start: 16 outliers final: 2 residues processed: 276 average time/residue: 0.6602 time to fit residues: 197.6989 Evaluate side-chains 193 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 1018 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 270 ASN A 777 GLN A 807 ASN B 850 GLN B 879 GLN C 850 GLN C 879 GLN D 850 GLN D1024 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106826 restraints weight = 26739.184| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.22 r_work: 0.2978 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15133 Z= 0.198 Angle : 0.655 7.108 20501 Z= 0.332 Chirality : 0.047 0.218 2252 Planarity : 0.005 0.064 2589 Dihedral : 10.637 167.239 2310 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.08 % Allowed : 20.01 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1859 helix: 1.59 (0.16), residues: 1012 sheet: 0.28 (0.45), residues: 141 loop : -0.01 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 995 TYR 0.021 0.003 TYR A 317 PHE 0.016 0.002 PHE B1061 TRP 0.013 0.002 TRP D 827 HIS 0.006 0.001 HIS A1072 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (15133) covalent geometry : angle 0.65453 / 0.33 (20501) hydrogen bonds : bond 0.05064 / 3.41 ( 782) hydrogen bonds : angle 5.05881 / 3.46 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6544 (mttm) cc_final: 0.5502 (tmtt) REVERT: A 53 GLN cc_start: 0.4623 (OUTLIER) cc_final: 0.4174 (pm20) REVERT: A 61 GLN cc_start: 0.7214 (mt0) cc_final: 0.6811 (mt0) REVERT: A 158 GLU cc_start: 0.6965 (pt0) cc_final: 0.6693 (pt0) REVERT: A 264 LEU cc_start: 0.7755 (mp) cc_final: 0.7502 (mt) REVERT: A 300 GLU cc_start: 0.6711 (tp30) cc_final: 0.6294 (tm-30) REVERT: A 316 THR cc_start: 0.7951 (m) cc_final: 0.7746 (t) REVERT: A 326 LEU cc_start: 0.7311 (mt) cc_final: 0.7002 (mt) REVERT: A 385 GLN cc_start: 0.7395 (pm20) cc_final: 0.7120 (pm20) REVERT: A 751 MET cc_start: 0.5834 (ppp) cc_final: 0.5499 (pmm) REVERT: A 978 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7362 (mptp) REVERT: A 996 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: B 985 MET cc_start: 0.8738 (mmm) cc_final: 0.8528 (mmp) REVERT: B 988 GLN cc_start: 0.8412 (tp40) cc_final: 0.7902 (mm110) REVERT: C 864 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8574 (mttm) REVERT: C 939 LEU cc_start: 0.9243 (mp) cc_final: 0.9007 (mt) REVERT: C 940 ASP cc_start: 0.8991 (t70) cc_final: 0.8783 (t70) REVERT: C 1067 MET cc_start: 0.8898 (ttm) cc_final: 0.8662 (mtm) REVERT: C 1078 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8264 (mtm180) REVERT: D 996 GLN cc_start: 0.7944 (mt0) cc_final: 0.7704 (pt0) REVERT: D 1089 ASP cc_start: 0.8474 (p0) cc_final: 0.8226 (p0) outliers start: 32 outliers final: 11 residues processed: 212 average time/residue: 0.6768 time to fit residues: 156.3852 Evaluate side-chains 195 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 866 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 81 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS ** A1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN C 850 GLN C 988 GLN D 850 GLN D1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110128 restraints weight = 21713.658| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.57 r_work: 0.3091 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15133 Z= 0.106 Angle : 0.522 6.987 20501 Z= 0.262 Chirality : 0.041 0.180 2252 Planarity : 0.004 0.058 2589 Dihedral : 9.782 162.803 2308 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.91 % Allowed : 20.53 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 1859 helix: 1.79 (0.16), residues: 1018 sheet: 0.31 (0.46), residues: 134 loop : -0.00 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 676 TYR 0.023 0.002 TYR A 252 PHE 0.023 0.001 PHE A 134 TRP 0.011 0.001 TRP A 84 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (15133) covalent geometry : angle 0.52226 / 0.26 (20501) hydrogen bonds : bond 0.03766 / 2.54 ( 782) hydrogen bonds : angle 4.58630 / 3.15 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6587 (mttm) cc_final: 0.5542 (tmtt) REVERT: A 61 GLN cc_start: 0.7112 (mt0) cc_final: 0.6685 (mt0) REVERT: A 158 GLU cc_start: 0.6895 (pt0) cc_final: 0.6660 (pt0) REVERT: A 204 PRO cc_start: 0.7395 (Cg_endo) cc_final: 0.6892 (Cg_exo) REVERT: A 264 LEU cc_start: 0.7753 (mp) cc_final: 0.7449 (mt) REVERT: A 316 THR cc_start: 0.7761 (m) cc_final: 0.7552 (t) REVERT: A 326 LEU cc_start: 0.7343 (mt) cc_final: 0.7054 (mt) REVERT: A 364 TYR cc_start: 0.5910 (t80) cc_final: 0.5309 (t80) REVERT: A 385 GLN cc_start: 0.7384 (pm20) cc_final: 0.7052 (pm20) REVERT: A 751 MET cc_start: 0.5829 (ppp) cc_final: 0.5467 (pmm) REVERT: A 864 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8537 (ttpt) REVERT: B 988 GLN cc_start: 0.8345 (tp40) cc_final: 0.7843 (mm110) REVERT: C 857 MET cc_start: 0.9111 (ttm) cc_final: 0.8800 (mtp) REVERT: C 864 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8487 (mttm) REVERT: C 939 LEU cc_start: 0.9161 (mp) cc_final: 0.8956 (mt) REVERT: C 1078 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8165 (mtm180) REVERT: D 1089 ASP cc_start: 0.8378 (p0) cc_final: 0.8131 (p0) outliers start: 14 outliers final: 7 residues processed: 195 average time/residue: 0.6753 time to fit residues: 143.3439 Evaluate side-chains 184 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 0.0010 chunk 183 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 overall best weight: 4.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 807 ASN B 850 GLN B 981 ASN C 850 GLN C 988 GLN D 850 GLN D 997 HIS D1024 ASN D1081 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103608 restraints weight = 24672.829| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.73 r_work: 0.2979 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15133 Z= 0.207 Angle : 0.641 7.351 20501 Z= 0.324 Chirality : 0.046 0.197 2252 Planarity : 0.005 0.051 2589 Dihedral : 10.302 166.318 2304 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.34 % Allowed : 18.97 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1859 helix: 1.55 (0.16), residues: 1014 sheet: 0.02 (0.44), residues: 141 loop : -0.05 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 976 TYR 0.023 0.003 TYR A 252 PHE 0.026 0.002 PHE A 134 TRP 0.010 0.002 TRP D 827 HIS 0.006 0.002 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (15133) covalent geometry : angle 0.64123 / 0.32 (20501) hydrogen bonds : bond 0.04993 / 3.34 ( 782) hydrogen bonds : angle 5.01900 / 3.43 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6617 (mttm) cc_final: 0.5496 (tmtt) REVERT: A 51 LEU cc_start: 0.4421 (OUTLIER) cc_final: 0.4177 (mt) REVERT: A 53 GLN cc_start: 0.4566 (OUTLIER) cc_final: 0.4087 (pm20) REVERT: A 61 GLN cc_start: 0.7130 (mt0) cc_final: 0.6669 (mt0) REVERT: A 140 VAL cc_start: 0.3426 (OUTLIER) cc_final: 0.3221 (t) REVERT: A 158 GLU cc_start: 0.6992 (pt0) cc_final: 0.6777 (pt0) REVERT: A 264 LEU cc_start: 0.7820 (mp) cc_final: 0.7537 (mt) REVERT: A 316 THR cc_start: 0.7974 (m) cc_final: 0.7751 (m) REVERT: A 385 GLN cc_start: 0.7360 (pm20) cc_final: 0.7044 (pm20) REVERT: A 732 LYS cc_start: 0.7955 (mttm) cc_final: 0.7687 (mttp) REVERT: A 751 MET cc_start: 0.6105 (ppp) cc_final: 0.5779 (pmm) REVERT: A 978 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7556 (mptp) REVERT: A 996 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: A 1050 GLU cc_start: 0.8737 (tt0) cc_final: 0.8521 (tp30) REVERT: B 881 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8165 (tpp80) REVERT: B 988 GLN cc_start: 0.8433 (tp40) cc_final: 0.7934 (mm110) REVERT: C 824 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6237 (m-30) REVERT: C 864 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8559 (mttm) REVERT: C 939 LEU cc_start: 0.9218 (mp) cc_final: 0.8992 (mt) REVERT: C 1078 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8191 (mtm180) REVERT: D 1089 ASP cc_start: 0.8474 (p0) cc_final: 0.8234 (p0) outliers start: 36 outliers final: 12 residues processed: 205 average time/residue: 0.7152 time to fit residues: 159.4024 Evaluate side-chains 195 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 HIS ** A1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN C 850 GLN C 988 GLN ** C1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108738 restraints weight = 29431.366| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.62 r_work: 0.2984 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15133 Z= 0.127 Angle : 0.548 7.080 20501 Z= 0.276 Chirality : 0.042 0.174 2252 Planarity : 0.004 0.052 2589 Dihedral : 9.838 163.965 2304 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.49 % Allowed : 20.08 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1859 helix: 1.72 (0.16), residues: 1021 sheet: 0.02 (0.45), residues: 136 loop : 0.00 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 995 TYR 0.030 0.002 TYR A 252 PHE 0.026 0.001 PHE A 134 TRP 0.010 0.001 TRP A 84 HIS 0.003 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15133) covalent geometry : angle 0.54777 / 0.28 (20501) hydrogen bonds : bond 0.04144 / 2.78 ( 782) hydrogen bonds : angle 4.75124 / 3.25 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6665 (mttm) cc_final: 0.5504 (tmtt) REVERT: A 53 GLN cc_start: 0.4611 (OUTLIER) cc_final: 0.4121 (pm20) REVERT: A 61 GLN cc_start: 0.7025 (mt0) cc_final: 0.6604 (mt0) REVERT: A 158 GLU cc_start: 0.6983 (pt0) cc_final: 0.6728 (pt0) REVERT: A 204 PRO cc_start: 0.7505 (Cg_endo) cc_final: 0.6970 (Cg_exo) REVERT: A 252 TYR cc_start: 0.7185 (t80) cc_final: 0.6850 (t80) REVERT: A 264 LEU cc_start: 0.7789 (mp) cc_final: 0.7558 (mm) REVERT: A 316 THR cc_start: 0.7819 (m) cc_final: 0.7594 (m) REVERT: A 751 MET cc_start: 0.6198 (ppp) cc_final: 0.5849 (pmm) REVERT: A 864 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8580 (ttpt) REVERT: A 996 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: B 988 GLN cc_start: 0.8486 (tp40) cc_final: 0.7945 (mm110) REVERT: C 824 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.6168 (m-30) REVERT: C 864 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (mttm) REVERT: C 939 LEU cc_start: 0.9173 (mp) cc_final: 0.8945 (mt) REVERT: C 1078 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8308 (mtm180) REVERT: D 1089 ASP cc_start: 0.8534 (p0) cc_final: 0.8275 (p0) outliers start: 23 outliers final: 10 residues processed: 192 average time/residue: 0.6481 time to fit residues: 135.9379 Evaluate side-chains 185 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 100 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 HIS A 807 ASN B 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105832 restraints weight = 19032.498| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.47 r_work: 0.3019 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15133 Z= 0.173 Angle : 0.608 7.228 20501 Z= 0.307 Chirality : 0.045 0.206 2252 Planarity : 0.004 0.050 2589 Dihedral : 10.005 164.828 2304 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.56 % Allowed : 20.21 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 1859 helix: 1.61 (0.16), residues: 1018 sheet: -0.05 (0.45), residues: 136 loop : -0.04 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 995 TYR 0.025 0.002 TYR A 252 PHE 0.027 0.002 PHE A 134 TRP 0.009 0.001 TRP D 827 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (15133) covalent geometry : angle 0.60817 / 0.31 (20501) hydrogen bonds : bond 0.04707 / 3.15 ( 782) hydrogen bonds : angle 4.93418 / 3.38 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6641 (mttm) cc_final: 0.6308 (mttp) REVERT: A 51 LEU cc_start: 0.4437 (OUTLIER) cc_final: 0.4200 (mt) REVERT: A 53 GLN cc_start: 0.4512 (OUTLIER) cc_final: 0.4126 (pm20) REVERT: A 61 GLN cc_start: 0.7067 (mt0) cc_final: 0.6612 (mt0) REVERT: A 158 GLU cc_start: 0.6945 (pt0) cc_final: 0.6728 (pt0) REVERT: A 204 PRO cc_start: 0.7378 (Cg_endo) cc_final: 0.6846 (Cg_exo) REVERT: A 264 LEU cc_start: 0.7851 (mp) cc_final: 0.7622 (mm) REVERT: A 316 THR cc_start: 0.7890 (m) cc_final: 0.7672 (m) REVERT: A 417 MET cc_start: 0.6802 (mtp) cc_final: 0.6593 (mtp) REVERT: A 732 LYS cc_start: 0.7913 (mttm) cc_final: 0.7634 (mttp) REVERT: A 751 MET cc_start: 0.6230 (ppp) cc_final: 0.5921 (pmm) REVERT: A 864 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8544 (ttpt) REVERT: A 996 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: B 988 GLN cc_start: 0.8385 (tp40) cc_final: 0.7958 (mm110) REVERT: C 824 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.6110 (m-30) REVERT: C 864 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8495 (mttm) REVERT: C 939 LEU cc_start: 0.9182 (mp) cc_final: 0.8973 (mt) REVERT: C 1078 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8121 (mtm180) REVERT: D 1089 ASP cc_start: 0.8388 (p0) cc_final: 0.8159 (p0) outliers start: 24 outliers final: 14 residues processed: 192 average time/residue: 0.6802 time to fit residues: 142.4458 Evaluate side-chains 192 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 HIS ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B 982 ASN C 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104996 restraints weight = 22248.408| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.52 r_work: 0.3001 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15133 Z= 0.191 Angle : 0.632 7.834 20501 Z= 0.319 Chirality : 0.045 0.169 2252 Planarity : 0.004 0.048 2589 Dihedral : 10.196 167.761 2304 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.88 % Allowed : 19.69 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1859 helix: 1.54 (0.16), residues: 1015 sheet: -0.13 (0.44), residues: 141 loop : -0.08 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 995 TYR 0.029 0.003 TYR A 252 PHE 0.026 0.002 PHE A 134 TRP 0.012 0.002 TRP D 827 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (15133) covalent geometry : angle 0.63185 / 0.32 (20501) hydrogen bonds : bond 0.04859 / 3.24 ( 782) hydrogen bonds : angle 5.01574 / 3.43 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6654 (mttm) cc_final: 0.5915 (mmmt) REVERT: A 53 GLN cc_start: 0.4821 (OUTLIER) cc_final: 0.4501 (pm20) REVERT: A 61 GLN cc_start: 0.7029 (mt0) cc_final: 0.6591 (mt0) REVERT: A 158 GLU cc_start: 0.7016 (pt0) cc_final: 0.6791 (pt0) REVERT: A 204 PRO cc_start: 0.7353 (Cg_endo) cc_final: 0.6862 (Cg_exo) REVERT: A 256 LEU cc_start: 0.7498 (mt) cc_final: 0.7030 (mt) REVERT: A 264 LEU cc_start: 0.7859 (mp) cc_final: 0.7618 (mm) REVERT: A 316 THR cc_start: 0.8011 (m) cc_final: 0.7799 (m) REVERT: A 732 LYS cc_start: 0.7920 (mttm) cc_final: 0.7641 (mttp) REVERT: A 751 MET cc_start: 0.6315 (ppp) cc_final: 0.6006 (pmt) REVERT: A 996 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: B 881 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8165 (tpp80) REVERT: B 988 GLN cc_start: 0.8466 (tp40) cc_final: 0.8002 (mm110) REVERT: C 824 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: C 864 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: C 939 LEU cc_start: 0.9177 (mp) cc_final: 0.8967 (mt) REVERT: C 1078 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8150 (mtm180) REVERT: D 1089 ASP cc_start: 0.8407 (p0) cc_final: 0.8182 (p0) outliers start: 29 outliers final: 13 residues processed: 192 average time/residue: 0.6899 time to fit residues: 144.6334 Evaluate side-chains 189 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 0.0060 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 HIS ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B 982 ASN ** B1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 988 GLN ** C1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107038 restraints weight = 31855.978| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.81 r_work: 0.2950 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15133 Z= 0.139 Angle : 0.575 11.266 20501 Z= 0.289 Chirality : 0.043 0.220 2252 Planarity : 0.004 0.048 2589 Dihedral : 9.893 167.356 2304 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.23 % Allowed : 20.47 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1859 helix: 1.69 (0.16), residues: 1019 sheet: -0.08 (0.45), residues: 136 loop : -0.04 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 995 TYR 0.018 0.002 TYR A 192 PHE 0.026 0.002 PHE A 134 TRP 0.013 0.001 TRP A 276 HIS 0.004 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15133) covalent geometry : angle 0.57543 / 0.29 (20501) hydrogen bonds : bond 0.04301 / 2.88 ( 782) hydrogen bonds : angle 4.82271 / 3.30 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6681 (mttm) cc_final: 0.5924 (mmmt) REVERT: A 61 GLN cc_start: 0.6946 (mt0) cc_final: 0.6528 (mt0) REVERT: A 158 GLU cc_start: 0.7033 (pt0) cc_final: 0.6777 (pt0) REVERT: A 204 PRO cc_start: 0.7434 (Cg_endo) cc_final: 0.6944 (Cg_exo) REVERT: A 256 LEU cc_start: 0.7426 (mt) cc_final: 0.7065 (mt) REVERT: A 264 LEU cc_start: 0.7835 (mp) cc_final: 0.7602 (mm) REVERT: A 316 THR cc_start: 0.7858 (m) cc_final: 0.7628 (m) REVERT: A 732 LYS cc_start: 0.7943 (mttm) cc_final: 0.7616 (mttp) REVERT: A 751 MET cc_start: 0.6320 (ppp) cc_final: 0.6054 (pmt) REVERT: A 864 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8583 (ttpt) REVERT: A 996 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: B 988 GLN cc_start: 0.8554 (tp40) cc_final: 0.7959 (mm110) REVERT: C 824 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: C 864 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (mttm) REVERT: C 939 LEU cc_start: 0.9164 (mp) cc_final: 0.8932 (mt) REVERT: C 1078 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8305 (mtm180) REVERT: D 1089 ASP cc_start: 0.8573 (p0) cc_final: 0.8315 (p0) outliers start: 19 outliers final: 11 residues processed: 186 average time/residue: 0.7234 time to fit residues: 146.3011 Evaluate side-chains 187 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 179 optimal weight: 7.9990 chunk 14 optimal weight: 0.0980 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 136 HIS ** A1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** B1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 988 GLN ** C1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.106808 restraints weight = 23928.301| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.62 r_work: 0.3035 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15133 Z= 0.127 Angle : 0.559 11.564 20501 Z= 0.281 Chirality : 0.042 0.249 2252 Planarity : 0.004 0.049 2589 Dihedral : 9.712 165.310 2304 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.43 % Allowed : 20.34 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1859 helix: 1.78 (0.16), residues: 1021 sheet: 0.01 (0.45), residues: 135 loop : -0.01 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 995 TYR 0.023 0.002 TYR A 304 PHE 0.025 0.001 PHE A 134 TRP 0.010 0.001 TRP B 827 HIS 0.003 0.001 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15133) covalent geometry : angle 0.55932 / 0.28 (20501) hydrogen bonds : bond 0.04125 / 2.76 ( 782) hydrogen bonds : angle 4.75250 / 3.26 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6675 (mttm) cc_final: 0.5934 (mmmt) REVERT: A 61 GLN cc_start: 0.7032 (mt0) cc_final: 0.6645 (mt0) REVERT: A 107 ILE cc_start: 0.5740 (mm) cc_final: 0.5351 (tt) REVERT: A 158 GLU cc_start: 0.6982 (pt0) cc_final: 0.6757 (pt0) REVERT: A 204 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.6956 (Cg_exo) REVERT: A 256 LEU cc_start: 0.7477 (mt) cc_final: 0.7121 (mt) REVERT: A 264 LEU cc_start: 0.7839 (mp) cc_final: 0.7599 (mm) REVERT: A 316 THR cc_start: 0.7805 (m) cc_final: 0.7516 (t) REVERT: A 732 LYS cc_start: 0.7892 (mttm) cc_final: 0.7570 (mttp) REVERT: A 751 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5990 (pmt) REVERT: A 864 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8538 (ttpt) REVERT: A 996 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: B 881 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8128 (tpp80) REVERT: B 988 GLN cc_start: 0.8434 (tp40) cc_final: 0.7837 (mm110) REVERT: C 824 ASP cc_start: 0.6183 (OUTLIER) cc_final: 0.5968 (m-30) REVERT: C 864 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8539 (mttm) REVERT: C 939 LEU cc_start: 0.9136 (mp) cc_final: 0.8933 (mt) REVERT: C 1078 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8184 (mtm180) REVERT: D 1089 ASP cc_start: 0.8378 (p0) cc_final: 0.8132 (p0) outliers start: 22 outliers final: 10 residues processed: 189 average time/residue: 0.6845 time to fit residues: 141.1369 Evaluate side-chains 185 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 866 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 22 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN B 850 GLN ** B1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105082 restraints weight = 23821.253| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.63 r_work: 0.3007 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15133 Z= 0.158 Angle : 0.600 11.632 20501 Z= 0.302 Chirality : 0.044 0.241 2252 Planarity : 0.004 0.048 2589 Dihedral : 9.926 167.250 2304 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.23 % Allowed : 20.53 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1859 helix: 1.67 (0.16), residues: 1018 sheet: -0.04 (0.44), residues: 140 loop : -0.00 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 995 TYR 0.018 0.002 TYR A 192 PHE 0.025 0.002 PHE A 134 TRP 0.014 0.001 TRP B 827 HIS 0.004 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15133) covalent geometry : angle 0.59962 / 0.30 (20501) hydrogen bonds : bond 0.04545 / 3.04 ( 782) hydrogen bonds : angle 4.89079 / 3.35 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6649 (mttm) cc_final: 0.5887 (mmmt) REVERT: A 61 GLN cc_start: 0.7072 (mt0) cc_final: 0.6676 (mt0) REVERT: A 107 ILE cc_start: 0.5772 (mm) cc_final: 0.5375 (tt) REVERT: A 158 GLU cc_start: 0.7003 (pt0) cc_final: 0.6771 (pt0) REVERT: A 204 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.6955 (Cg_exo) REVERT: A 256 LEU cc_start: 0.7484 (mt) cc_final: 0.7122 (mt) REVERT: A 264 LEU cc_start: 0.7862 (mp) cc_final: 0.7628 (mm) REVERT: A 316 THR cc_start: 0.7849 (m) cc_final: 0.7649 (m) REVERT: A 732 LYS cc_start: 0.7895 (mttm) cc_final: 0.7607 (mttp) REVERT: A 751 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.6022 (pmt) REVERT: A 864 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8559 (ttpt) REVERT: A 996 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: B 881 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8146 (tpp80) REVERT: B 988 GLN cc_start: 0.8465 (tp40) cc_final: 0.7881 (mm110) REVERT: C 824 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6044 (m-30) REVERT: C 864 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8564 (mttm) REVERT: C 939 LEU cc_start: 0.9170 (mp) cc_final: 0.8958 (mt) REVERT: C 1078 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8159 (mtm180) REVERT: D 1089 ASP cc_start: 0.8428 (p0) cc_final: 0.8198 (p0) outliers start: 19 outliers final: 11 residues processed: 183 average time/residue: 0.7043 time to fit residues: 140.6350 Evaluate side-chains 188 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 100 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** B1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 988 GLN ** C1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106312 restraints weight = 22429.484| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.57 r_work: 0.3024 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15133 Z= 0.143 Angle : 0.582 11.892 20501 Z= 0.293 Chirality : 0.043 0.238 2252 Planarity : 0.004 0.048 2589 Dihedral : 9.911 167.468 2304 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.23 % Allowed : 20.40 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 1859 helix: 1.69 (0.16), residues: 1025 sheet: -0.01 (0.44), residues: 140 loop : 0.02 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 995 TYR 0.022 0.002 TYR A 304 PHE 0.025 0.002 PHE A 134 TRP 0.012 0.001 TRP B 827 HIS 0.003 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15133) covalent geometry : angle 0.58201 / 0.29 (20501) hydrogen bonds : bond 0.04350 / 2.91 ( 782) hydrogen bonds : angle 4.83344 / 3.31 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7875.20 seconds wall clock time: 134 minutes 32.31 seconds (8072.31 seconds total)