Starting phenix.real_space_refine on Fri Jul 3 15:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5d_29740/07_2026/8g5d_29740.cif" } resolution = 2.5 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= 0.001 sd= 0.170 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 102 5.16 5 C 9433 2.51 5 N 2507 2.21 5 O 2792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 14852 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 8012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1037, 8009 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 987} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1037, 8009 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 987} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8180 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 152 Unusual residues: {'ACO': 1, 'ADP': 1, 'OAA': 1, 'PO4': 1, 'Q5B': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.38, per 1000 atoms: 0.29 Number of scatterers: 14852 At special positions: 0 Unit cell: (131.97, 112.05, 133.63, 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 102 16.00 P 18 15.00 O 2792 8.00 N 2507 7.00 C 9433 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: 1.31 Conformation dependent library (CDL) restraints added in 841.5 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 20 sheets defined 55.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... 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 953 removed outlier: 3.608A pdb=" N GLY A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 966 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.545A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1016 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: 3.849A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.977A 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 removed outlier: 3.580A pdb=" N LEU B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 868 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 953 removed outlier: 3.605A pdb=" N GLY B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 966 Processing helix chain 'B' and resid 986 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: 3.834A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.890A 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 831 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 953 removed outlier: 3.547A pdb=" N GLY C 953 " --> pdb=" O ALA C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 966 Processing helix chain 'C' and resid 986 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 Processing helix chain 'C' and resid 1055 through 1080 removed outlier: 3.941A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.030A 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 7 through 19 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.581A pdb=" N SER D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 removed outlier: 4.145A pdb=" N LYS D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.530A pdb=" N GLU D 118 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 4.338A pdb=" N ASP D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY D 143 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 177 through 195 Processing helix chain 'D' and resid 224 through 228 removed outlier: 4.350A pdb=" N TYR D 227 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 312 through 328 Processing helix chain 'D' and resid 349 through 364 Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 383 through 398 removed outlier: 3.505A pdb=" N GLY D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.510A pdb=" N ALA D 559 " --> pdb=" O ASN D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 586 removed outlier: 4.725A pdb=" N TYR D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 664 through 678 Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.519A pdb=" N HIS D 700 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.730A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.520A pdb=" N ALA D 749 " --> pdb=" O GLY D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 783 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 806 Processing helix chain 'D' and resid 825 through 831 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 953 removed outlier: 3.635A pdb=" N GLY D 953 " --> pdb=" O ALA D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 966 Processing helix chain 'D' and resid 986 through 998 Processing helix chain 'D' and resid 1001 through 1018 Processing helix chain 'D' and resid 1024 through 1040 Processing helix chain 'D' and resid 1044 through 1055 Processing helix chain 'D' and resid 1055 through 1080 removed outlier: 3.848A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.992A 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 823 through 824 removed outlier: 6.682A pdb=" N MET A 823 " --> pdb=" O ARG B 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 834 through 835 Processing sheet with id=AA3, first strand: chain 'A' and resid 840 through 842 removed outlier: 6.605A pdb=" N PHE A 840 " --> pdb=" O SER D1092 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 845 through 846 Processing sheet with id=AA5, first strand: chain 'A' and resid 1091 through 1093 Processing sheet with id=AA6, first strand: chain 'B' and resid 840 through 842 removed outlier: 6.638A pdb=" N PHE B 840 " --> pdb=" O SER C1092 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 845 through 846 Processing sheet with id=AA8, first strand: chain 'B' and resid 1091 through 1093 Processing sheet with id=AA9, first strand: chain 'C' and resid 823 through 824 removed outlier: 6.523A pdb=" N MET C 823 " --> pdb=" O ARG D 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 834 through 835 Processing sheet with id=AB2, first strand: chain 'C' and resid 845 through 846 Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.643A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.643A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.033A pdb=" N LEU D 55 " --> pdb=" O ASN D 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 95 Processing sheet with id=AB7, first strand: chain 'D' and resid 263 through 268 Processing sheet with id=AB8, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.671A pdb=" N TRP D 276 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.198A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 499 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL D 530 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL D 501 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE D 594 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 634 through 635 removed outlier: 6.957A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU D 716 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 660 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 845 through 846 768 hydrogen bonds defined for protein. 2232 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: 2.69 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2463 1.32 - 1.46: 4517 1.46 - 1.59: 7955 1.59 - 1.73: 33 1.73 - 1.86: 168 Bond restraints: 15136 Sorted by residual: bond pdb=" C5 Q5B D3303 " pdb=" C6 Q5B D3303 " ideal model delta sigma weight residual 1.539 1.317 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C18 Q5B D3303 " pdb=" N6 Q5B D3303 " ideal model delta sigma weight residual 1.337 1.491 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C5A ACO A3301 " pdb=" C6A ACO A3301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5A ACO C3301 " pdb=" C6A ACO C3301 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C2P ACO C3301 " pdb=" S1P ACO C3301 " ideal model delta sigma weight residual 1.818 1.747 0.071 1.00e-02 1.00e+04 5.10e+01 ... (remaining 15131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 20260 3.49 - 6.98: 192 6.98 - 10.47: 34 10.47 - 13.96: 10 13.96 - 17.45: 6 Bond angle restraints: 20502 Sorted by residual: angle pdb=" P1A ACO C3301 " pdb=" O3A ACO C3301 " pdb=" P2A ACO C3301 " ideal model delta sigma weight residual 136.83 124.29 12.54 1.00e+00 1.00e+00 1.57e+02 angle pdb=" P1A ACO D3301 " pdb=" O3A ACO D3301 " pdb=" P2A ACO D3301 " ideal model delta sigma weight residual 136.83 124.98 11.85 1.00e+00 1.00e+00 1.40e+02 angle pdb=" P1A ACO B3301 " pdb=" O3A ACO B3301 " pdb=" P2A ACO B3301 " ideal model delta sigma weight residual 136.83 125.32 11.51 1.00e+00 1.00e+00 1.33e+02 angle pdb=" P1A ACO A3301 " pdb=" O3A ACO A3301 " pdb=" P2A ACO A3301 " ideal model delta sigma weight residual 136.83 126.80 10.03 1.00e+00 1.00e+00 1.01e+02 angle pdb=" C5A ACO A3301 " pdb=" C4A ACO A3301 " pdb=" N3A ACO A3301 " ideal model delta sigma weight residual 126.80 118.57 8.23 1.00e+00 1.00e+00 6.77e+01 ... (remaining 20497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 8583 35.76 - 71.51: 297 71.51 - 107.27: 37 107.27 - 143.02: 1 143.02 - 178.78: 6 Dihedral angle restraints: 8924 sinusoidal: 3600 harmonic: 5324 Sorted by residual: dihedral pdb=" C5' ADP D3304 " pdb=" O5' ADP D3304 " pdb=" PA ADP D3304 " pdb=" O2A ADP D3304 " ideal model delta sinusoidal sigma weight residual 300.00 138.11 161.90 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D3304 " pdb=" O3A ADP D3304 " pdb=" PA ADP D3304 " pdb=" PB ADP D3304 " ideal model delta sinusoidal sigma weight residual -60.00 70.69 -130.69 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP D3304 " pdb=" O3A ADP D3304 " pdb=" PB ADP D3304 " pdb=" PA ADP D3304 " ideal model delta sinusoidal sigma weight residual -60.00 47.07 -107.07 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 8921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1919 0.070 - 0.139: 311 0.139 - 0.209: 17 0.209 - 0.279: 6 0.279 - 0.348: 1 Chirality restraints: 2254 Sorted by residual: chirality pdb=" C7 Q5B D3303 " pdb=" C6 Q5B D3303 " pdb=" C8 Q5B D3303 " pdb=" O8 Q5B D3303 " both_signs ideal model delta sigma weight residual False 2.49 2.84 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA THR D1014 " pdb=" N THR D1014 " pdb=" C THR D1014 " pdb=" CB THR D1014 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LYS D1012 " pdb=" N LYS D1012 " pdb=" C LYS D1012 " pdb=" CB LYS D1012 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2251 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO B3301 " -0.211 2.00e-02 2.50e+03 1.81e-01 4.07e+02 pdb=" C5P ACO B3301 " 0.050 2.00e-02 2.50e+03 pdb=" C6P ACO B3301 " 0.037 2.00e-02 2.50e+03 pdb=" N4P ACO B3301 " 0.293 2.00e-02 2.50e+03 pdb=" O5P ACO B3301 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO D3301 " 0.155 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C5P ACO D3301 " -0.045 2.00e-02 2.50e+03 pdb=" C6P ACO D3301 " 0.116 2.00e-02 2.50e+03 pdb=" N4P ACO D3301 " -0.199 2.00e-02 2.50e+03 pdb=" O5P ACO D3301 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C3301 " -0.138 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C9P ACO C3301 " 0.048 2.00e-02 2.50e+03 pdb=" CAP ACO C3301 " -0.106 2.00e-02 2.50e+03 pdb=" N8P ACO C3301 " 0.179 2.00e-02 2.50e+03 pdb=" O9P ACO C3301 " 0.017 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1677 2.75 - 3.28: 14766 3.28 - 3.82: 27028 3.82 - 4.36: 33633 4.36 - 4.90: 55039 Nonbonded interactions: 132143 Sorted by model distance: nonbonded pdb=" OE1 GLU A 847 " pdb=" NH2 ARG D1085 " model vdw 2.207 3.120 nonbonded pdb=" O LEU D 85 " pdb=" N LEU D 89 " model vdw 2.228 3.120 nonbonded pdb=" OG SER B 843 " pdb=" OD1 ASP D1075 " model vdw 2.242 3.040 nonbonded pdb=" O GLY D 664 " pdb=" OG SER D 667 " model vdw 2.242 3.040 nonbonded pdb=" O LYS D 265 " pdb=" OH TYR D 319 " model vdw 2.252 3.040 ... (remaining 132138 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 'A' selection = chain 'B' selection = chain 'C' } 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: 0.610 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.007 0.222 15136 Z= 0.417 Angle : 0.941 17.455 20502 Z= 0.521 Chirality : 0.051 0.348 2254 Planarity : 0.008 0.181 2595 Dihedral : 18.553 178.781 5538 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.52 % Allowed : 21.61 % Favored : 77.87 % 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: 0.68 (0.19), residues: 1865 helix: 1.12 (0.16), residues: 1004 sheet: 0.16 (0.44), residues: 143 loop : -0.33 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 389 TYR 0.017 0.003 TYR D 120 PHE 0.020 0.002 PHE D 189 TRP 0.023 0.003 TRP A 827 HIS 0.007 0.002 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.42 (15136) covalent geometry : angle 0.94147 / 0.52 (20502) hydrogen bonds : bond 0.09654 / 6.09 ( 764) hydrogen bonds : angle 5.29880 / 3.81 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.572 Fit side-chains REVERT: A 940 ASP cc_start: 0.7420 (t70) cc_final: 0.7186 (t70) REVERT: A 965 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6742 (mttt) REVERT: A 1089 ASP cc_start: 0.7386 (p0) cc_final: 0.7042 (p0) REVERT: A 1094 VAL cc_start: 0.8575 (t) cc_final: 0.8337 (m) REVERT: B 965 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7884 (ttmm) REVERT: B 1089 ASP cc_start: 0.7418 (p0) cc_final: 0.7001 (p0) REVERT: C 866 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6701 (mp0) REVERT: D 56 VAL cc_start: 0.7269 (p) cc_final: 0.7032 (p) REVERT: D 107 ILE cc_start: 0.8074 (mt) cc_final: 0.7873 (mm) REVERT: D 788 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7337 (ttt90) REVERT: D 820 THR cc_start: 0.8075 (m) cc_final: 0.7856 (t) REVERT: D 864 LYS cc_start: 0.7442 (mtpt) cc_final: 0.7005 (tttp) outliers start: 8 outliers final: 1 residues processed: 203 average time/residue: 0.6499 time to fit residues: 143.2708 Evaluate side-chains 187 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 961 ASN A1020 ASN A1058 ASN B 982 ASN B1024 ASN C 961 ASN C1024 ASN D 27 ASN D 45 GLN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 299 ASN D 757 GLN D 982 ASN D1024 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118433 restraints weight = 19881.478| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.53 r_work: 0.3177 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15136 Z= 0.145 Angle : 0.578 9.603 20502 Z= 0.298 Chirality : 0.044 0.282 2254 Planarity : 0.005 0.074 2595 Dihedral : 11.930 175.525 2111 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.94 % Allowed : 18.41 % Favored : 78.66 % 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: 0.84 (0.20), residues: 1865 helix: 1.25 (0.16), residues: 1008 sheet: -0.03 (0.43), residues: 143 loop : -0.19 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 881 TYR 0.013 0.002 TYR D 120 PHE 0.014 0.002 PHE D1061 TRP 0.021 0.002 TRP D 40 HIS 0.006 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15136) covalent geometry : angle 0.57782 / 0.30 (20502) hydrogen bonds : bond 0.04188 / 2.83 ( 764) hydrogen bonds : angle 4.72147 / 3.39 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 867 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7731 (ptm) REVERT: A 888 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8219 (mm-40) REVERT: A 996 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: B 888 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: B 1089 ASP cc_start: 0.8409 (p0) cc_final: 0.8188 (p0) REVERT: C 1050 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: D 40 TRP cc_start: 0.6837 (m100) cc_final: 0.6608 (m100) REVERT: D 103 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7221 (pttm) REVERT: D 121 VAL cc_start: 0.8523 (t) cc_final: 0.8266 (p) REVERT: D 230 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7866 (ttpt) REVERT: D 732 LYS cc_start: 0.8445 (tppp) cc_final: 0.8239 (tppp) REVERT: D 757 GLN cc_start: 0.7843 (tp40) cc_final: 0.7641 (tp-100) REVERT: D 848 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7407 (ptt-90) outliers start: 45 outliers final: 10 residues processed: 232 average time/residue: 0.6428 time to fit residues: 161.9808 Evaluate side-chains 199 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 82 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.0670 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN A1058 ASN A1081 GLN C1020 ASN C1024 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116699 restraints weight = 23036.325| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.66 r_work: 0.3164 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15136 Z= 0.137 Angle : 0.551 8.340 20502 Z= 0.284 Chirality : 0.043 0.256 2254 Planarity : 0.004 0.063 2595 Dihedral : 11.599 172.553 2104 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.55 % Allowed : 18.47 % Favored : 78.98 % 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: 0.91 (0.20), residues: 1865 helix: 1.33 (0.16), residues: 1009 sheet: -0.03 (0.44), residues: 142 loop : -0.19 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1085 TYR 0.016 0.002 TYR D 213 PHE 0.013 0.001 PHE D1061 TRP 0.017 0.001 TRP D 40 HIS 0.004 0.001 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15136) covalent geometry : angle 0.55145 / 0.28 (20502) hydrogen bonds : bond 0.03943 / 2.68 ( 764) hydrogen bonds : angle 4.55854 / 3.27 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 867 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7688 (ptm) REVERT: A 888 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8171 (mm-40) REVERT: A 965 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7539 (mttt) REVERT: A 996 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: B 888 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: B 948 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8865 (tttt) REVERT: B 965 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8775 (ttmm) REVERT: B 1089 ASP cc_start: 0.8452 (p0) cc_final: 0.8174 (p0) REVERT: C 866 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: C 1050 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: D 103 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7195 (pttm) REVERT: D 121 VAL cc_start: 0.8546 (t) cc_final: 0.8325 (p) REVERT: D 230 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7900 (ttpt) REVERT: D 327 MET cc_start: 0.8441 (ttm) cc_final: 0.8186 (mtm) REVERT: D 835 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6937 (tpp-160) outliers start: 39 outliers final: 13 residues processed: 211 average time/residue: 0.6520 time to fit residues: 149.2883 Evaluate side-chains 200 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 167 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN B1024 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.150033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117989 restraints weight = 23062.932| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.68 r_work: 0.3180 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15136 Z= 0.118 Angle : 0.530 8.599 20502 Z= 0.271 Chirality : 0.042 0.253 2254 Planarity : 0.004 0.055 2595 Dihedral : 11.232 169.825 2104 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.61 % Allowed : 18.47 % Favored : 78.92 % 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: 1.02 (0.20), residues: 1865 helix: 1.43 (0.16), residues: 1010 sheet: -0.05 (0.44), residues: 144 loop : -0.16 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1085 TYR 0.018 0.001 TYR D 213 PHE 0.011 0.001 PHE B1061 TRP 0.019 0.001 TRP D 40 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15136) covalent geometry : angle 0.53023 / 0.27 (20502) hydrogen bonds : bond 0.03644 / 2.48 ( 764) hydrogen bonds : angle 4.41501 / 3.16 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 823 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5268 (ttp) REVERT: A 881 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8315 (tmm-80) REVERT: A 888 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8133 (mm-40) REVERT: A 965 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7528 (mttt) REVERT: A 996 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: B 888 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: B 891 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 948 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8838 (tttt) REVERT: B 965 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8731 (ttmm) REVERT: B 1089 ASP cc_start: 0.8477 (p0) cc_final: 0.8202 (p0) REVERT: D 103 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7152 (ptpp) REVERT: D 107 ILE cc_start: 0.8338 (mt) cc_final: 0.8136 (mm) REVERT: D 230 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (ttpt) REVERT: D 835 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6857 (tpp-160) REVERT: D 848 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7467 (ptt-90) REVERT: D 940 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7893 (t70) outliers start: 40 outliers final: 19 residues processed: 213 average time/residue: 0.6272 time to fit residues: 145.0389 Evaluate side-chains 208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 940 ASP Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 0.0870 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119407 restraints weight = 18085.568| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.47 r_work: 0.3193 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15136 Z= 0.121 Angle : 0.529 9.451 20502 Z= 0.270 Chirality : 0.042 0.253 2254 Planarity : 0.004 0.051 2595 Dihedral : 10.947 167.469 2104 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.13 % Allowed : 18.15 % Favored : 78.72 % 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: 1.11 (0.20), residues: 1865 helix: 1.52 (0.16), residues: 1004 sheet: 0.01 (0.44), residues: 145 loop : -0.13 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 881 TYR 0.014 0.001 TYR D 213 PHE 0.011 0.001 PHE D1061 TRP 0.014 0.001 TRP D 40 HIS 0.004 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15136) covalent geometry : angle 0.52915 / 0.27 (20502) hydrogen bonds : bond 0.03647 / 2.48 ( 764) hydrogen bonds : angle 4.38716 / 3.13 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 881 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8299 (tmm-80) REVERT: A 888 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: A 965 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7510 (mttt) REVERT: A 976 ARG cc_start: 0.7030 (ptt-90) cc_final: 0.6645 (ptp90) REVERT: A 996 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7326 (mt0) REVERT: B 888 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: B 891 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8391 (mt-10) REVERT: B 948 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8833 (tttt) REVERT: B 965 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8715 (ttmm) REVERT: B 1089 ASP cc_start: 0.8493 (p0) cc_final: 0.8207 (p0) REVERT: D 103 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7226 (pttm) REVERT: D 135 HIS cc_start: 0.7918 (t70) cc_final: 0.7599 (t70) REVERT: D 230 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7893 (ttpt) REVERT: D 327 MET cc_start: 0.8491 (mtm) cc_final: 0.8036 (mtm) REVERT: D 835 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6850 (tpp-160) REVERT: D 848 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7538 (ptt-90) REVERT: D 940 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7842 (t70) outliers start: 48 outliers final: 21 residues processed: 221 average time/residue: 0.6335 time to fit residues: 151.9410 Evaluate side-chains 209 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 940 ASP Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN C1024 ASN D 45 GLN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN D1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117161 restraints weight = 18033.130| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.53 r_work: 0.3154 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15136 Z= 0.142 Angle : 0.549 9.710 20502 Z= 0.282 Chirality : 0.043 0.258 2254 Planarity : 0.004 0.048 2595 Dihedral : 10.923 165.719 2104 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.81 % Allowed : 18.60 % Favored : 78.59 % 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: 1.09 (0.20), residues: 1865 helix: 1.48 (0.16), residues: 1004 sheet: 0.02 (0.45), residues: 144 loop : -0.11 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1085 TYR 0.013 0.002 TYR D 213 PHE 0.011 0.002 PHE D 189 TRP 0.015 0.001 TRP D 40 HIS 0.004 0.001 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15136) covalent geometry : angle 0.54948 / 0.28 (20502) hydrogen bonds : bond 0.03908 / 2.66 ( 764) hydrogen bonds : angle 4.47553 / 3.20 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 881 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8327 (tmm-80) REVERT: A 888 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: A 965 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7545 (mptt) REVERT: A 976 ARG cc_start: 0.7029 (ptt-90) cc_final: 0.6651 (ptp90) REVERT: A 996 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: B 835 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7196 (tpp-160) REVERT: B 888 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: B 891 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8474 (mt-10) REVERT: B 948 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8844 (tttt) REVERT: B 1089 ASP cc_start: 0.8532 (p0) cc_final: 0.8319 (p0) REVERT: D 103 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7297 (pttm) REVERT: D 135 HIS cc_start: 0.7967 (t70) cc_final: 0.7668 (t70) REVERT: D 230 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7930 (ttpt) REVERT: D 327 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: D 835 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6850 (tpp-160) REVERT: D 848 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7514 (ptt-90) outliers start: 43 outliers final: 20 residues processed: 204 average time/residue: 0.6841 time to fit residues: 150.8735 Evaluate side-chains 205 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN C1024 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN D1024 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115004 restraints weight = 16210.818| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.41 r_work: 0.3119 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15136 Z= 0.179 Angle : 0.590 9.061 20502 Z= 0.303 Chirality : 0.045 0.271 2254 Planarity : 0.004 0.047 2595 Dihedral : 11.007 164.464 2104 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.81 % Allowed : 18.60 % Favored : 78.59 % 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: 0.95 (0.20), residues: 1865 helix: 1.38 (0.16), residues: 1004 sheet: 0.01 (0.44), residues: 144 loop : -0.21 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 389 TYR 0.014 0.002 TYR D 213 PHE 0.015 0.002 PHE D 189 TRP 0.015 0.001 TRP D 40 HIS 0.005 0.001 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (15136) covalent geometry : angle 0.59015 / 0.30 (20502) hydrogen bonds : bond 0.04302 / 2.93 ( 764) hydrogen bonds : angle 4.63191 / 3.32 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 823 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5580 (ttp) REVERT: A 881 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8428 (tmm-80) REVERT: A 888 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: A 965 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7569 (mptt) REVERT: A 976 ARG cc_start: 0.7069 (ptt-90) cc_final: 0.6685 (ptp90) REVERT: A 996 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7815 (mp10) REVERT: A 1009 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 835 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7201 (mmp80) REVERT: B 888 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8393 (mm-40) REVERT: B 948 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8893 (tttt) REVERT: B 965 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8467 (tptp) REVERT: D 103 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7408 (pttm) REVERT: D 327 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8210 (mtm) REVERT: D 835 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6901 (tpp-160) REVERT: D 848 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7513 (ptt-90) REVERT: D 940 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7957 (t70) REVERT: D 978 LYS cc_start: 0.6694 (mtmm) cc_final: 0.6425 (mtmt) outliers start: 43 outliers final: 22 residues processed: 208 average time/residue: 0.6904 time to fit residues: 155.7534 Evaluate side-chains 208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 940 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN C 975 HIS C 996 GLN C1024 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 GLN D1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119310 restraints weight = 18382.288| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.52 r_work: 0.3168 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15136 Z= 0.110 Angle : 0.525 10.065 20502 Z= 0.267 Chirality : 0.042 0.248 2254 Planarity : 0.004 0.046 2595 Dihedral : 10.650 161.541 2104 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.35 % Allowed : 19.13 % Favored : 78.52 % 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: 1.14 (0.20), residues: 1865 helix: 1.54 (0.16), residues: 1004 sheet: 0.05 (0.44), residues: 144 loop : -0.11 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 881 TYR 0.010 0.001 TYR D 192 PHE 0.012 0.001 PHE B1061 TRP 0.015 0.001 TRP D 40 HIS 0.004 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15136) covalent geometry : angle 0.52474 / 0.27 (20502) hydrogen bonds : bond 0.03546 / 2.41 ( 764) hydrogen bonds : angle 4.35541 / 3.11 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 823 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5620 (ttp) REVERT: A 881 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8320 (tmm-80) REVERT: A 888 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: A 965 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7533 (mttt) REVERT: A 976 ARG cc_start: 0.6977 (ptt-90) cc_final: 0.6574 (ptp90) REVERT: A 996 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: A 1009 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 835 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7100 (mmp80) REVERT: B 888 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: B 948 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8884 (tttt) REVERT: B 965 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8391 (tptp) REVERT: D 103 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7354 (pttm) REVERT: D 135 HIS cc_start: 0.7897 (t70) cc_final: 0.7647 (t70) REVERT: D 327 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8223 (mtm) REVERT: D 835 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6806 (tpp-160) REVERT: D 848 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7625 (ptt-90) outliers start: 36 outliers final: 20 residues processed: 196 average time/residue: 0.6371 time to fit residues: 134.8837 Evaluate side-chains 204 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 148 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 overall best weight: 2.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN C 975 HIS C 996 GLN C1020 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 757 GLN D1020 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116106 restraints weight = 19609.738| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.49 r_work: 0.3135 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15136 Z= 0.153 Angle : 0.567 9.734 20502 Z= 0.289 Chirality : 0.044 0.260 2254 Planarity : 0.004 0.046 2595 Dihedral : 10.775 161.140 2104 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.42 % Allowed : 19.19 % Favored : 78.39 % 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: 1.12 (0.20), residues: 1865 helix: 1.50 (0.16), residues: 1004 sheet: 0.07 (0.44), residues: 144 loop : -0.10 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1085 TYR 0.012 0.002 TYR D 213 PHE 0.013 0.002 PHE D 189 TRP 0.015 0.001 TRP D 40 HIS 0.010 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (15136) covalent geometry : angle 0.56685 / 0.29 (20502) hydrogen bonds : bond 0.04007 / 2.73 ( 764) hydrogen bonds : angle 4.48913 / 3.21 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 823 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.5639 (ttp) REVERT: A 881 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8426 (tmm-80) REVERT: A 888 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8192 (mm-40) REVERT: A 965 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7537 (mptt) REVERT: A 976 ARG cc_start: 0.7001 (ptt-90) cc_final: 0.6640 (ptp90) REVERT: A 996 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: A 1009 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 835 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7182 (mmp80) REVERT: B 888 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: B 891 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 948 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8869 (tttt) REVERT: B 965 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8405 (tptp) REVERT: D 103 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7373 (pttm) REVERT: D 327 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8215 (mtm) REVERT: D 835 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6889 (tpp-160) REVERT: D 848 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7542 (ptt-90) REVERT: D 940 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7906 (t70) REVERT: D 978 LYS cc_start: 0.6568 (mtmm) cc_final: 0.6312 (mttt) outliers start: 37 outliers final: 21 residues processed: 199 average time/residue: 0.6617 time to fit residues: 142.6048 Evaluate side-chains 206 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 940 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN C 975 HIS C 996 GLN C1020 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116873 restraints weight = 20131.965| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.52 r_work: 0.3146 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15136 Z= 0.136 Angle : 0.555 9.952 20502 Z= 0.282 Chirality : 0.043 0.259 2254 Planarity : 0.004 0.050 2595 Dihedral : 10.694 160.252 2104 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.22 % Allowed : 19.45 % Favored : 78.33 % 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: 1.12 (0.20), residues: 1865 helix: 1.51 (0.16), residues: 1004 sheet: 0.06 (0.44), residues: 144 loop : -0.11 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1085 TYR 0.010 0.002 TYR D 131 PHE 0.011 0.001 PHE B1061 TRP 0.014 0.001 TRP D 40 HIS 0.010 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15136) covalent geometry : angle 0.55523 / 0.28 (20502) hydrogen bonds : bond 0.03868 / 2.63 ( 764) hydrogen bonds : angle 4.45669 / 3.19 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 823 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5651 (ttp) REVERT: A 867 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7701 (ptm) REVERT: A 881 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8376 (tmm-80) REVERT: A 888 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8199 (mm-40) REVERT: A 965 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7527 (mptt) REVERT: A 976 ARG cc_start: 0.6957 (ptt-90) cc_final: 0.6593 (ptp90) REVERT: A 996 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: A 1009 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 835 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7179 (mmp80) REVERT: B 888 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8319 (mp10) REVERT: B 891 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 948 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8901 (tttt) REVERT: B 965 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8380 (tptp) REVERT: D 103 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7398 (pttm) REVERT: D 327 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8224 (mtm) REVERT: D 835 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6790 (tpp-160) REVERT: D 848 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7573 (ptt-90) outliers start: 34 outliers final: 21 residues processed: 196 average time/residue: 0.6715 time to fit residues: 142.2127 Evaluate side-chains 204 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.0040 chunk 111 optimal weight: 0.9980 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 ASN C 975 HIS C 996 GLN C1020 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118121 restraints weight = 24108.049| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.74 r_work: 0.3165 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15136 Z= 0.112 Angle : 0.531 9.939 20502 Z= 0.268 Chirality : 0.042 0.251 2254 Planarity : 0.004 0.049 2595 Dihedral : 10.512 158.803 2104 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 19.58 % Favored : 78.26 % 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: 1.22 (0.20), residues: 1865 helix: 1.61 (0.16), residues: 1003 sheet: 0.00 (0.43), residues: 148 loop : -0.08 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1085 TYR 0.011 0.001 TYR D 192 PHE 0.012 0.001 PHE B1061 TRP 0.017 0.001 TRP D 40 HIS 0.010 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15136) covalent geometry : angle 0.53093 / 0.27 (20502) hydrogen bonds : bond 0.03559 / 2.42 ( 764) hydrogen bonds : angle 4.32629 / 3.09 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5900.44 seconds wall clock time: 100 minutes 52.91 seconds (6052.91 seconds total)