Starting phenix.real_space_refine on Fri Mar 6 13:01:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6poe_20413/03_2026/6poe_20413_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6poe_20413/03_2026/6poe_20413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6poe_20413/03_2026/6poe_20413_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6poe_20413/03_2026/6poe_20413_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6poe_20413/03_2026/6poe_20413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6poe_20413/03_2026/6poe_20413.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.005 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 12 5.49 5 S 180 5.16 5 C 20334 2.51 5 N 5387 2.21 5 O 5899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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: 8059 Chain: "B" Number of atoms: 7903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7895 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7895 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8056 Chain: "C" Number of atoms: 7902 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7894 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7894 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8055 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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: 8059 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'COA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'COA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 13.85, per 1000 atoms: 0.44 Number of scatterers: 31812 At special positions: 0 Unit cell: (141.81, 163.56, 173.13, 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 180 16.00 P 12 15.00 O 5899 8.00 N 5387 7.00 C 20334 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: 2.75 Conformation dependent library (CDL) restraints added in 2.7 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 35 sheets defined 45.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 177 through 196 removed outlier: 4.055A pdb=" N ALA A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 7.094A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 282 through 294 removed outlier: 4.036A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.845A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.548A pdb=" N GLY A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.907A pdb=" N ALA A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.663A pdb=" N HIS A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 Processing helix chain 'A' and resid 771 through 782 removed outlier: 3.943A pdb=" N GLU A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 807 Processing helix chain 'A' and resid 824 through 832 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 883 through 897 removed outlier: 3.537A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 937 through 952 removed outlier: 3.512A pdb=" N ALA A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.912A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1015 removed outlier: 3.808A pdb=" N ASP A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 3.786A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1055 Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 4.259A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 3.586A pdb=" N ILE A1091 " --> pdb=" O TRP A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 39 through 47 removed outlier: 3.684A pdb=" N LEU B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 4.012A pdb=" N GLN B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.649A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.549A pdb=" N GLY B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.846A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.930A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.949A pdb=" N GLY B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 removed outlier: 3.930A pdb=" N LEU B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.688A pdb=" N ALA B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 664 through 678 removed outlier: 4.144A pdb=" N ASN B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.850A pdb=" N HIS B 700 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 removed outlier: 3.689A pdb=" N ILE B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 781 removed outlier: 3.673A pdb=" N GLU B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 808 Processing helix chain 'B' and resid 824 through 831 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 877 removed outlier: 3.527A pdb=" N VAL B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 897 removed outlier: 3.721A pdb=" N GLN B 888 " --> pdb=" O LYS B 884 " (cutoff:3.500A) 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 949 removed outlier: 3.554A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 967 removed outlier: 3.508A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 998 Processing helix chain 'B' and resid 1001 through 1018 removed outlier: 3.666A pdb=" N ASP B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 4.433A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1054 removed outlier: 3.969A pdb=" N ASP B1053 " --> pdb=" O ASP B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1079 removed outlier: 3.883A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1091 removed outlier: 3.568A pdb=" N ILE B1091 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.609A pdb=" N ILE C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 4.207A pdb=" N LEU C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 180 through 194 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.542A pdb=" N CYS C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.562A pdb=" N SER C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 327 Processing helix chain 'C' and resid 349 through 364 removed outlier: 4.011A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.626A pdb=" N LEU C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 398 Processing helix chain 'C' and resid 412 through 419 removed outlier: 4.172A pdb=" N LEU C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.642A pdb=" N ALA C 559 " --> pdb=" O ASN C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 664 through 678 removed outlier: 4.176A pdb=" N ASN C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU C 669 " --> pdb=" O GLY C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 706 removed outlier: 3.719A pdb=" N HIS C 700 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 706 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 734 Processing helix chain 'C' and resid 771 through 781 removed outlier: 3.573A pdb=" N GLU C 781 " --> pdb=" O GLN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 806 Processing helix chain 'C' and resid 824 through 832 Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 868 through 879 Processing helix chain 'C' and resid 883 through 897 removed outlier: 3.502A pdb=" N GLN C 888 " --> pdb=" O LYS C 884 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 889 " --> pdb=" O TYR C 885 " (cutoff:3.500A) 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 949 removed outlier: 4.237A pdb=" N ALA C 941 " --> pdb=" O GLY C 937 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 943 " --> pdb=" O LEU C 939 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 966 removed outlier: 3.793A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 995 removed outlier: 4.189A pdb=" N GLN C 988 " --> pdb=" O ASP C 984 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.019A pdb=" N ASP C1005 " --> pdb=" O THR C1001 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1039 removed outlier: 4.628A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1054 removed outlier: 4.129A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1079 removed outlier: 3.763A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1091 removed outlier: 3.618A pdb=" N ILE C1091 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 40 through 47 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 180 through 194 Processing helix chain 'D' and resid 225 through 228 removed outlier: 3.549A pdb=" N ILE D 228 " --> pdb=" O ALA D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 228' Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.689A pdb=" N SER D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 349 through 363 removed outlier: 4.146A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 412 through 418 Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.607A pdb=" N ALA D 559 " --> pdb=" O ASN D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 587 removed outlier: 3.678A pdb=" N SER D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN D 587 " --> pdb=" O MET D 583 " (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 665 through 678 removed outlier: 4.409A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.994A pdb=" N HIS D 700 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 Processing helix chain 'D' and resid 771 through 781 Processing helix chain 'D' and resid 792 through 807 Processing helix chain 'D' and resid 825 through 831 Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 879 removed outlier: 3.643A pdb=" N VAL D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 897 removed outlier: 3.592A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 889 " --> pdb=" O TYR D 885 " (cutoff:3.500A) 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 951 removed outlier: 3.740A pdb=" N ALA D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 943 " --> pdb=" O LEU D 939 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 966 removed outlier: 3.672A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 998 removed outlier: 4.089A pdb=" N LEU D 990 " --> pdb=" O ARG D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1015 removed outlier: 3.838A pdb=" N ASP D1005 " --> pdb=" O THR D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 4.496A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1055 removed outlier: 3.769A pdb=" N ASP D1053 " --> pdb=" O ASP D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1079 removed outlier: 3.658A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 removed outlier: 3.545A pdb=" N ILE D1091 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.421A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 199 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA A 125 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU A 201 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 123 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 203 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 121 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.421A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.051A pdb=" N LEU A 55 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.857A pdb=" N TRP A 276 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 336 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N PHE A 376 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG A 378 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 340 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 543 removed outlier: 7.457A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS A 498 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE A 570 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 500 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 630 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 686 removed outlier: 6.766A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 713 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TRP A 743 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 715 " --> pdb=" O TRP A 743 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.819A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE B 119 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.819A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 34 removed outlier: 5.627A pdb=" N LEU B 55 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AB5, first strand: chain 'B' and resid 263 through 268 Processing sheet with id=AB6, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.853A pdb=" N ILE B 375 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE B 405 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 377 " --> pdb=" O PHE B 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 537 through 543 removed outlier: 7.302A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 500 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 594 " --> pdb=" O THR B 619 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 681 through 686 removed outlier: 6.671A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLU B 718 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 713 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TRP B 743 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 715 " --> pdb=" O TRP B 743 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 745 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY B 717 " --> pdb=" O ILE B 745 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 973 through 974 Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.153A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.854A pdb=" N VAL C 214 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.104A pdb=" N VAL C 57 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL C 74 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AC5, first strand: chain 'C' and resid 263 through 268 Processing sheet with id=AC6, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.631A pdb=" N TRP C 276 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 537 through 543 removed outlier: 7.367A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS C 498 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 568 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 634 through 635 removed outlier: 4.464A pdb=" N GLY C 627 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 716 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 660 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLU C 718 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 713 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N TRP C 743 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL C 715 " --> pdb=" O TRP C 743 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE C 745 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLY C 717 " --> pdb=" O ILE C 745 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.121A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.121A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 32 through 34 Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 95 Processing sheet with id=AD4, first strand: chain 'D' and resid 263 through 268 Processing sheet with id=AD5, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.328A pdb=" N TRP D 276 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.114A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 629 through 630 Processing sheet with id=AD8, first strand: chain 'D' and resid 681 through 686 removed outlier: 6.724A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE D 745 " --> pdb=" O VAL D 715 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY D 717 " --> pdb=" O ILE D 745 " (cutoff:3.500A) 1409 hydrogen bonds defined for protein. 4053 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: 7.93 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5258 1.30 - 1.43: 8105 1.43 - 1.56: 18811 1.56 - 1.69: 43 1.69 - 1.82: 292 Bond restraints: 32509 Sorted by residual: bond pdb=" C1B COA B1202 " pdb=" C2B COA B1202 " ideal model delta sigma weight residual 1.533 1.319 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1B COA C1201 " pdb=" C2B COA C1201 " ideal model delta sigma weight residual 1.533 1.322 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C1B COA B1201 " pdb=" O4B COA B1201 " ideal model delta sigma weight residual 1.418 1.628 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C1B COA C1202 " pdb=" O4B COA C1202 " ideal model delta sigma weight residual 1.418 1.627 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C1B COA B1201 " pdb=" C2B COA B1201 " ideal model delta sigma weight residual 1.533 1.326 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 32504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 43592 3.46 - 6.92: 382 6.92 - 10.37: 58 10.37 - 13.83: 11 13.83 - 17.29: 9 Bond angle restraints: 44052 Sorted by residual: angle pdb=" C ASN D 981 " pdb=" N ASN D 982 " pdb=" CA ASN D 982 " ideal model delta sigma weight residual 122.37 131.17 -8.80 9.30e-01 1.16e+00 8.95e+01 angle pdb=" C GLY A 622 " pdb=" N PRO A 623 " pdb=" CA PRO A 623 " ideal model delta sigma weight residual 119.84 131.09 -11.25 1.25e+00 6.40e-01 8.10e+01 angle pdb=" C ILE B 834 " pdb=" N ARG B 835 " pdb=" CA ARG B 835 " ideal model delta sigma weight residual 121.54 134.07 -12.53 1.91e+00 2.74e-01 4.31e+01 angle pdb=" C VAL B1094 " pdb=" N LEU B1095 " pdb=" CA LEU B1095 " ideal model delta sigma weight residual 120.51 129.30 -8.79 1.45e+00 4.76e-01 3.67e+01 angle pdb=" N1A COA B1202 " pdb=" C6A COA B1202 " pdb=" N6A COA B1202 " ideal model delta sigma weight residual 119.19 101.90 17.29 3.00e+00 1.11e-01 3.32e+01 ... (remaining 44047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 17289 17.85 - 35.70: 1609 35.70 - 53.55: 495 53.55 - 71.40: 117 71.40 - 89.25: 44 Dihedral angle restraints: 19554 sinusoidal: 7914 harmonic: 11640 Sorted by residual: dihedral pdb=" CA GLY B 622 " pdb=" C GLY B 622 " pdb=" N PRO B 623 " pdb=" CA PRO B 623 " ideal model delta harmonic sigma weight residual -180.00 -133.44 -46.56 0 5.00e+00 4.00e-02 8.67e+01 dihedral pdb=" CA GLY C 622 " pdb=" C GLY C 622 " pdb=" N PRO C 623 " pdb=" CA PRO C 623 " ideal model delta harmonic sigma weight residual -180.00 -136.12 -43.88 0 5.00e+00 4.00e-02 7.70e+01 dihedral pdb=" CA GLY D 622 " pdb=" C GLY D 622 " pdb=" N PRO D 623 " pdb=" CA PRO D 623 " ideal model delta harmonic sigma weight residual -180.00 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 ... (remaining 19551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4541 0.099 - 0.197: 351 0.197 - 0.296: 12 0.296 - 0.395: 6 0.395 - 0.494: 1 Chirality restraints: 4911 Sorted by residual: chirality pdb=" CB ILE B 834 " pdb=" CA ILE B 834 " pdb=" CG1 ILE B 834 " pdb=" CG2 ILE B 834 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA THR A 842 " pdb=" N THR A 842 " pdb=" C THR A 842 " pdb=" CB THR A 842 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 4908 not shown) Planarity restraints: 5624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 854 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C TYR A 854 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 854 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 855 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B1018 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO B1019 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B1019 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1019 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 601 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO D 602 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 602 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 602 " 0.038 5.00e-02 4.00e+02 ... (remaining 5621 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 427 2.62 - 3.19: 26069 3.19 - 3.76: 49903 3.76 - 4.33: 68086 4.33 - 4.90: 115153 Nonbonded interactions: 259638 Sorted by model distance: nonbonded pdb=" CB PRO A 623 " pdb=" OD2 ASP A 690 " model vdw 2.049 3.440 nonbonded pdb=" O GLU A1011 " pdb=" OG1 THR A1015 " model vdw 2.207 3.040 nonbonded pdb=" O ALA A 624 " pdb=" N GLY A 689 " model vdw 2.213 3.120 nonbonded pdb=" O CYS C 893 " pdb=" OG1 THR C 897 " model vdw 2.242 3.040 nonbonded pdb=" O LEU B 324 " pdb=" OG1 THR B 328 " model vdw 2.279 3.040 ... (remaining 259633 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' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) or re \ sid 981 through 1016 or (resid 1017 and (name N or name CA or name C or name O o \ r name CB )) or resid 1018 through 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1016 or (resid 1017 and (name N or name CA or name C or name O or name CB )) or \ resid 1018 through 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) or re \ sid 981 through 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) or re \ sid 981 through 1016 or (resid 1017 and (name N or name CA or name C or name O o \ r name CB )) or resid 1018 through 1099)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 40.140 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.009 0.214 32509 Z= 0.398 Angle : 0.951 17.289 44052 Z= 0.508 Chirality : 0.056 0.494 4911 Planarity : 0.007 0.070 5624 Dihedral : 16.225 89.250 12162 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.24 % Favored : 92.61 % Rotamer: Outliers : 11.53 % Allowed : 11.56 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.08 % 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: -4.29 (0.10), residues: 4068 helix: -2.67 (0.09), residues: 1761 sheet: -2.53 (0.18), residues: 637 loop : -3.00 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 848 TYR 0.025 0.002 TYR C 213 PHE 0.022 0.002 PHE A 191 TRP 0.012 0.001 TRP C 84 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00875 (32509) covalent geometry : angle 0.95091 (44052) hydrogen bonds : bond 0.08443 ( 1389) hydrogen bonds : angle 6.22551 ( 4053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 386 poor density : 537 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8425 (tp) cc_final: 0.8205 (pt) REVERT: A 97 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7712 (tmmt) REVERT: A 175 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: A 190 ASN cc_start: 0.7242 (t0) cc_final: 0.6850 (t0) REVERT: A 409 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8704 (m) REVERT: A 507 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: A 666 MET cc_start: 0.8200 (mmm) cc_final: 0.7860 (mmt) REVERT: A 1001 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8229 (t) REVERT: A 1035 ASP cc_start: 0.7824 (t70) cc_final: 0.7433 (t0) REVERT: A 1036 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.8020 (ttm) REVERT: A 1075 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 25 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6613 (tp) REVERT: B 386 GLU cc_start: 0.7804 (tt0) cc_final: 0.7476 (tm-30) REVERT: B 391 MET cc_start: 0.8813 (tpp) cc_final: 0.8537 (tpt) REVERT: B 411 MET cc_start: 0.8584 (ttt) cc_final: 0.8233 (ttt) REVERT: B 567 ASP cc_start: 0.8149 (t70) cc_final: 0.7795 (t0) REVERT: B 965 LYS cc_start: 0.8752 (tptt) cc_final: 0.8519 (mttm) REVERT: B 1075 ASP cc_start: 0.8450 (t0) cc_final: 0.8224 (t0) REVERT: C 29 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5558 (m-10) REVERT: C 391 MET cc_start: 0.8250 (tpp) cc_final: 0.7713 (tpt) REVERT: C 393 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6435 (tm-30) REVERT: C 516 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: C 597 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8859 (mm) REVERT: C 729 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6784 (mtt180) REVERT: C 866 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: C 873 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 1051 TYR cc_start: 0.8766 (m-80) cc_final: 0.8456 (m-80) REVERT: C 1054 ILE cc_start: 0.8604 (mm) cc_final: 0.8308 (pt) REVERT: C 1075 ASP cc_start: 0.8459 (t0) cc_final: 0.8128 (t0) REVERT: D 91 GLN cc_start: 0.4845 (OUTLIER) cc_final: 0.4561 (mp10) REVERT: D 106 LEU cc_start: 0.2269 (OUTLIER) cc_final: 0.1842 (tp) REVERT: D 154 VAL cc_start: 0.2869 (OUTLIER) cc_final: 0.2624 (p) REVERT: D 242 PHE cc_start: 0.2716 (OUTLIER) cc_final: 0.1238 (t80) REVERT: D 274 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.3658 (ptm-80) REVERT: D 389 ARG cc_start: 0.6216 (ttp80) cc_final: 0.5852 (ttm-80) REVERT: D 869 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8721 (mp) REVERT: D 1035 ASP cc_start: 0.7619 (t0) cc_final: 0.7211 (t0) REVERT: D 1036 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8220 (ttm) REVERT: D 1050 GLU cc_start: 0.7442 (tt0) cc_final: 0.6836 (mt-10) outliers start: 386 outliers final: 153 residues processed: 871 average time/residue: 0.2145 time to fit residues: 298.1911 Evaluate side-chains 561 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 389 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1009 GLU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 567 ASP Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 839 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1036 MET Chi-restraints excluded: chain D residue 1040 CYS Chi-restraints excluded: chain D residue 1075 ASP Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0270 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 45 GLN A 332 HIS A 537 HIS A 555 ASN A 587 ASN A 638 ASN A 705 GLN A 807 ASN A 908 HIS A 961 ASN B 53 GLN B 161 ASN B 403 HIS B 571 ASN B 587 ASN B 638 ASN B 767 GLN B 777 GLN B 850 GLN B 908 HIS B 988 GLN B1020 ASN C 638 ASN C 705 GLN C 767 GLN C 888 GLN C 900 HIS C 988 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS D 54 ASN D 75 ASN D 332 HIS ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 410 HIS D 545 HIS D 645 ASN D 888 GLN D 908 HIS D 961 ASN D 988 GLN D1020 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143569 restraints weight = 66321.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139028 restraints weight = 66905.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135102 restraints weight = 49080.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134142 restraints weight = 54195.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133316 restraints weight = 42464.593| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32509 Z= 0.126 Angle : 0.623 10.502 44052 Z= 0.326 Chirality : 0.045 0.264 4911 Planarity : 0.005 0.057 5624 Dihedral : 10.257 97.283 4957 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 5.08 % Allowed : 17.35 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.12), residues: 4068 helix: -1.00 (0.11), residues: 1773 sheet: -2.19 (0.20), residues: 578 loop : -2.70 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 995 TYR 0.024 0.001 TYR C 213 PHE 0.025 0.001 PHE B 110 TRP 0.010 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00285 (32509) covalent geometry : angle 0.62251 (44052) hydrogen bonds : bond 0.03537 ( 1389) hydrogen bonds : angle 5.04557 ( 4053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 437 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7061 (mm) cc_final: 0.6813 (mt) REVERT: A 97 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7609 (tmmt) REVERT: A 151 LYS cc_start: 0.7517 (mttm) cc_final: 0.7266 (mttt) REVERT: A 175 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: A 190 ASN cc_start: 0.7265 (t0) cc_final: 0.6876 (t0) REVERT: A 385 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7927 (mm-40) REVERT: A 507 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7298 (ttt180) REVERT: A 961 ASN cc_start: 0.8656 (m-40) cc_final: 0.8429 (m-40) REVERT: A 1001 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7858 (t) REVERT: A 1035 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7191 (t0) REVERT: B 25 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6920 (tp) REVERT: B 339 ILE cc_start: 0.8827 (mm) cc_final: 0.8624 (mt) REVERT: B 386 GLU cc_start: 0.7496 (tt0) cc_final: 0.7204 (tm-30) REVERT: B 391 MET cc_start: 0.8869 (tpp) cc_final: 0.8628 (tpt) REVERT: B 411 MET cc_start: 0.8650 (ttt) cc_final: 0.8208 (ttt) REVERT: B 567 ASP cc_start: 0.7955 (t70) cc_final: 0.7616 (t0) REVERT: C 389 ARG cc_start: 0.7253 (ttp-170) cc_final: 0.6933 (ttm-80) REVERT: C 391 MET cc_start: 0.8586 (tpp) cc_final: 0.8364 (tpt) REVERT: C 848 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8170 (pmt-80) REVERT: C 866 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: C 873 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 1051 TYR cc_start: 0.8572 (m-80) cc_final: 0.8286 (m-80) REVERT: D 91 GLN cc_start: 0.4540 (OUTLIER) cc_final: 0.4217 (mp10) REVERT: D 106 LEU cc_start: 0.2989 (OUTLIER) cc_final: 0.2698 (tp) REVERT: D 242 PHE cc_start: 0.2557 (OUTLIER) cc_final: 0.1063 (t80) REVERT: D 274 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.3757 (ptm-80) REVERT: D 389 ARG cc_start: 0.6526 (ttp80) cc_final: 0.6009 (ttm-80) REVERT: D 403 HIS cc_start: 0.5613 (m90) cc_final: 0.5098 (t-90) REVERT: D 1035 ASP cc_start: 0.7525 (t0) cc_final: 0.7172 (t0) REVERT: D 1050 GLU cc_start: 0.7048 (tt0) cc_final: 0.6803 (tt0) outliers start: 171 outliers final: 110 residues processed: 583 average time/residue: 0.2025 time to fit residues: 192.4695 Evaluate side-chains 503 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 380 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 324 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 282 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS A 590 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 150 GLN B 767 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 332 HIS C 410 HIS C 638 ASN C 908 HIS C 975 HIS C1020 ASN C1024 ASN C1086 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D1086 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137612 restraints weight = 74962.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133082 restraints weight = 85722.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130285 restraints weight = 59674.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131035 restraints weight = 59262.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131525 restraints weight = 36933.691| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32509 Z= 0.195 Angle : 0.638 10.862 44052 Z= 0.331 Chirality : 0.047 0.288 4911 Planarity : 0.005 0.057 5624 Dihedral : 9.278 84.987 4835 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.65 % Favored : 93.33 % Rotamer: Outliers : 5.08 % Allowed : 17.77 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.12), residues: 4068 helix: -0.40 (0.12), residues: 1776 sheet: -2.02 (0.20), residues: 584 loop : -2.57 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 359 TYR 0.020 0.002 TYR B 192 PHE 0.020 0.001 PHE B 110 TRP 0.023 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00464 (32509) covalent geometry : angle 0.63791 (44052) hydrogen bonds : bond 0.03660 ( 1389) hydrogen bonds : angle 4.89291 ( 4053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 391 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7084 (mm) cc_final: 0.6855 (mt) REVERT: A 97 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7606 (tmmt) REVERT: A 151 LYS cc_start: 0.7479 (mttm) cc_final: 0.7256 (mttt) REVERT: A 175 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: A 190 ASN cc_start: 0.7390 (t0) cc_final: 0.7010 (t0) REVERT: A 385 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (mm-40) REVERT: A 961 ASN cc_start: 0.8716 (m-40) cc_final: 0.8505 (m-40) REVERT: A 1001 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7905 (t) REVERT: A 1035 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7221 (t0) REVERT: B 25 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6959 (tp) REVERT: B 69 LEU cc_start: 0.8031 (tt) cc_final: 0.7692 (mt) REVERT: B 339 ILE cc_start: 0.8885 (mm) cc_final: 0.8647 (mt) REVERT: B 386 GLU cc_start: 0.7544 (tt0) cc_final: 0.7266 (tm-30) REVERT: B 560 MET cc_start: 0.9000 (mmm) cc_final: 0.8272 (mmm) REVERT: B 567 ASP cc_start: 0.8049 (t70) cc_final: 0.7473 (t0) REVERT: B 824 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: B 925 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8442 (m) REVERT: C 389 ARG cc_start: 0.7277 (ttp-170) cc_final: 0.6849 (ttm-80) REVERT: C 585 THR cc_start: 0.8846 (m) cc_final: 0.8645 (p) REVERT: C 848 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8353 (pmt-80) REVERT: C 866 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: C 1075 ASP cc_start: 0.8720 (t0) cc_final: 0.8434 (t0) REVERT: D 91 GLN cc_start: 0.4487 (OUTLIER) cc_final: 0.4145 (mp10) REVERT: D 106 LEU cc_start: 0.3224 (OUTLIER) cc_final: 0.2947 (tp) REVERT: D 242 PHE cc_start: 0.2530 (OUTLIER) cc_final: 0.0874 (t80) REVERT: D 389 ARG cc_start: 0.6510 (ttp80) cc_final: 0.5929 (ttm-80) REVERT: D 403 HIS cc_start: 0.5648 (m90) cc_final: 0.4969 (t-90) REVERT: D 1035 ASP cc_start: 0.7606 (t0) cc_final: 0.7207 (t0) outliers start: 171 outliers final: 122 residues processed: 536 average time/residue: 0.1987 time to fit residues: 175.2313 Evaluate side-chains 499 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 365 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1013 ILE Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 387 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 348 optimal weight: 20.0000 chunk 276 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 169 optimal weight: 0.0270 chunk 74 optimal weight: 6.9990 overall best weight: 3.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 53 GLN B 410 HIS C 26 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 383 ASN D 545 HIS D 981 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142690 restraints weight = 76058.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136318 restraints weight = 76835.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134436 restraints weight = 71114.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134886 restraints weight = 58018.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134696 restraints weight = 44045.070| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32509 Z= 0.162 Angle : 0.610 9.603 44052 Z= 0.316 Chirality : 0.046 0.236 4911 Planarity : 0.004 0.056 5624 Dihedral : 8.740 89.466 4809 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 5.17 % Allowed : 18.06 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % 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: -1.98 (0.13), residues: 4068 helix: -0.07 (0.12), residues: 1776 sheet: -1.92 (0.20), residues: 590 loop : -2.42 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 359 TYR 0.019 0.001 TYR D 307 PHE 0.019 0.001 PHE C 347 TRP 0.025 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00383 (32509) covalent geometry : angle 0.60994 (44052) hydrogen bonds : bond 0.03456 ( 1389) hydrogen bonds : angle 4.73406 ( 4053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 395 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7154 (mm) cc_final: 0.6907 (mt) REVERT: A 97 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7641 (tmmt) REVERT: A 151 LYS cc_start: 0.7374 (mttm) cc_final: 0.7153 (mttt) REVERT: A 175 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: A 190 ASN cc_start: 0.7331 (t0) cc_final: 0.6966 (t0) REVERT: A 385 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: A 847 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: A 921 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8760 (p) REVERT: A 961 ASN cc_start: 0.8702 (m-40) cc_final: 0.8501 (m-40) REVERT: A 1001 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7907 (t) REVERT: A 1035 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7159 (t0) REVERT: B 25 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6685 (tp) REVERT: B 339 ILE cc_start: 0.8872 (mm) cc_final: 0.8622 (mt) REVERT: B 386 GLU cc_start: 0.7563 (tt0) cc_final: 0.7328 (tm-30) REVERT: B 560 MET cc_start: 0.8804 (mmm) cc_final: 0.8194 (mmm) REVERT: B 565 GLU cc_start: 0.7627 (pm20) cc_final: 0.7249 (pm20) REVERT: B 567 ASP cc_start: 0.8029 (t70) cc_final: 0.7781 (t70) REVERT: B 779 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7872 (mp) REVERT: C 50 LEU cc_start: 0.5871 (mm) cc_final: 0.5592 (mt) REVERT: C 389 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.6974 (ttm-80) REVERT: C 585 THR cc_start: 0.8870 (m) cc_final: 0.8669 (p) REVERT: C 848 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8247 (pmt-80) REVERT: C 866 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: C 1040 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7850 (p) REVERT: C 1075 ASP cc_start: 0.8532 (t0) cc_final: 0.8269 (t0) REVERT: D 91 GLN cc_start: 0.4613 (OUTLIER) cc_final: 0.4224 (mp10) REVERT: D 106 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2860 (tp) REVERT: D 242 PHE cc_start: 0.2403 (OUTLIER) cc_final: 0.0683 (t80) REVERT: D 368 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4907 (mm) REVERT: D 389 ARG cc_start: 0.6512 (ttp80) cc_final: 0.5920 (ttm-80) REVERT: D 403 HIS cc_start: 0.5607 (m90) cc_final: 0.5087 (t-90) REVERT: D 1035 ASP cc_start: 0.7471 (t0) cc_final: 0.7103 (t0) REVERT: D 1046 GLU cc_start: 0.7183 (mp0) cc_final: 0.6811 (mp0) REVERT: D 1050 GLU cc_start: 0.7115 (tt0) cc_final: 0.6516 (mt-10) REVERT: D 1067 MET cc_start: 0.8095 (mtt) cc_final: 0.7804 (mtm) outliers start: 174 outliers final: 128 residues processed: 537 average time/residue: 0.1853 time to fit residues: 164.6693 Evaluate side-chains 518 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 375 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 346 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 366 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 389 optimal weight: 0.6980 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS B 53 GLN B 961 ASN C 47 HIS C 671 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142546 restraints weight = 57081.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136964 restraints weight = 53787.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129888 restraints weight = 57968.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129335 restraints weight = 66030.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128374 restraints weight = 52180.401| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32509 Z= 0.161 Angle : 0.607 11.270 44052 Z= 0.313 Chirality : 0.046 0.263 4911 Planarity : 0.004 0.058 5624 Dihedral : 8.491 87.966 4800 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.58 % Favored : 93.40 % Rotamer: Outliers : 5.05 % Allowed : 18.39 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % 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: -1.76 (0.13), residues: 4068 helix: 0.14 (0.12), residues: 1776 sheet: -1.86 (0.20), residues: 596 loop : -2.30 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 359 TYR 0.020 0.001 TYR D 307 PHE 0.014 0.001 PHE A 29 TRP 0.026 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00382 (32509) covalent geometry : angle 0.60733 (44052) hydrogen bonds : bond 0.03414 ( 1389) hydrogen bonds : angle 4.67009 ( 4053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 391 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7091 (mm) cc_final: 0.6833 (mt) REVERT: A 97 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7592 (tmmt) REVERT: A 175 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: A 190 ASN cc_start: 0.7375 (t0) cc_final: 0.7003 (t0) REVERT: A 330 GLU cc_start: 0.5851 (mp0) cc_final: 0.5563 (mp0) REVERT: A 847 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: A 921 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 961 ASN cc_start: 0.8713 (m-40) cc_final: 0.8493 (m-40) REVERT: A 1001 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 1035 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7150 (t0) REVERT: B 25 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6786 (tp) REVERT: B 339 ILE cc_start: 0.8866 (mm) cc_final: 0.8629 (mt) REVERT: B 386 GLU cc_start: 0.7557 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 560 MET cc_start: 0.8746 (mmm) cc_final: 0.8125 (mmm) REVERT: B 565 GLU cc_start: 0.7708 (pm20) cc_final: 0.7407 (pm20) REVERT: B 567 ASP cc_start: 0.8056 (t70) cc_final: 0.7489 (t0) REVERT: B 779 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7904 (mp) REVERT: C 389 ARG cc_start: 0.7342 (ttp-170) cc_final: 0.6909 (ttm-80) REVERT: C 671 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7831 (m-40) REVERT: C 848 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8233 (pmt-80) REVERT: C 866 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: C 1040 CYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7783 (p) REVERT: C 1075 ASP cc_start: 0.8606 (t0) cc_final: 0.8334 (t0) REVERT: D 91 GLN cc_start: 0.4554 (OUTLIER) cc_final: 0.4182 (mp10) REVERT: D 106 LEU cc_start: 0.3474 (OUTLIER) cc_final: 0.3176 (tp) REVERT: D 242 PHE cc_start: 0.2242 (OUTLIER) cc_final: 0.0518 (t80) REVERT: D 368 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4910 (mm) REVERT: D 389 ARG cc_start: 0.6453 (ttp80) cc_final: 0.5827 (ttm-80) REVERT: D 403 HIS cc_start: 0.5627 (m90) cc_final: 0.5068 (t-90) REVERT: D 1035 ASP cc_start: 0.7518 (t0) cc_final: 0.7165 (t0) REVERT: D 1046 GLU cc_start: 0.6984 (mp0) cc_final: 0.6776 (mp0) REVERT: D 1050 GLU cc_start: 0.7003 (tt0) cc_final: 0.6618 (mt-10) REVERT: D 1067 MET cc_start: 0.8109 (mtt) cc_final: 0.7809 (mtm) outliers start: 170 outliers final: 120 residues processed: 527 average time/residue: 0.1922 time to fit residues: 166.9045 Evaluate side-chains 505 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 370 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 174 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 180 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 404 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN C 671 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.175819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143064 restraints weight = 65462.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137628 restraints weight = 68597.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134523 restraints weight = 60046.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133514 restraints weight = 55461.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131502 restraints weight = 50307.791| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32509 Z= 0.132 Angle : 0.588 13.951 44052 Z= 0.302 Chirality : 0.045 0.247 4911 Planarity : 0.004 0.057 5624 Dihedral : 8.165 86.404 4787 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 4.28 % Allowed : 19.34 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % 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: -1.54 (0.13), residues: 4068 helix: 0.31 (0.12), residues: 1779 sheet: -1.75 (0.21), residues: 596 loop : -2.19 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 359 TYR 0.020 0.001 TYR D 307 PHE 0.012 0.001 PHE B 191 TRP 0.028 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00310 (32509) covalent geometry : angle 0.58774 (44052) hydrogen bonds : bond 0.03234 ( 1389) hydrogen bonds : angle 4.58984 ( 4053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 398 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7171 (mm) cc_final: 0.6966 (mt) REVERT: A 97 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7582 (tmmt) REVERT: A 175 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: A 190 ASN cc_start: 0.7298 (t0) cc_final: 0.6942 (t0) REVERT: A 330 GLU cc_start: 0.5775 (mp0) cc_final: 0.5508 (mp0) REVERT: A 839 SER cc_start: 0.7132 (OUTLIER) cc_final: 0.6335 (m) REVERT: A 961 ASN cc_start: 0.8662 (m-40) cc_final: 0.8447 (m-40) REVERT: A 1001 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 1035 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7114 (t0) REVERT: B 25 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6729 (tp) REVERT: B 339 ILE cc_start: 0.8853 (mm) cc_final: 0.8611 (mt) REVERT: B 386 GLU cc_start: 0.7562 (tt0) cc_final: 0.7322 (tm-30) REVERT: B 560 MET cc_start: 0.8765 (mmm) cc_final: 0.8098 (mmm) REVERT: B 567 ASP cc_start: 0.8036 (t70) cc_final: 0.7798 (t70) REVERT: B 779 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7842 (mp) REVERT: B 973 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 50 LEU cc_start: 0.5842 (mm) cc_final: 0.5637 (mt) REVERT: C 389 ARG cc_start: 0.7310 (ttp-170) cc_final: 0.6965 (ttm-80) REVERT: C 848 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8264 (pmt-80) REVERT: C 866 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: C 1040 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7683 (p) REVERT: C 1075 ASP cc_start: 0.8616 (t0) cc_final: 0.8341 (t0) REVERT: D 106 LEU cc_start: 0.3486 (OUTLIER) cc_final: 0.3162 (tp) REVERT: D 242 PHE cc_start: 0.2297 (OUTLIER) cc_final: 0.0578 (t80) REVERT: D 368 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.4913 (mm) REVERT: D 389 ARG cc_start: 0.6476 (ttp80) cc_final: 0.5853 (ttm-80) REVERT: D 403 HIS cc_start: 0.5635 (m90) cc_final: 0.5146 (t-90) REVERT: D 1035 ASP cc_start: 0.7417 (t0) cc_final: 0.7080 (t0) REVERT: D 1050 GLU cc_start: 0.6955 (tt0) cc_final: 0.6610 (mt-10) REVERT: D 1067 MET cc_start: 0.8036 (mtt) cc_final: 0.7809 (mtm) outliers start: 144 outliers final: 111 residues processed: 513 average time/residue: 0.1864 time to fit residues: 156.2464 Evaluate side-chains 503 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 379 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 289 optimal weight: 0.7980 chunk 375 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 283 optimal weight: 0.0970 chunk 373 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 358 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 271 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS C 555 ASN C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.178329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145873 restraints weight = 78086.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140697 restraints weight = 77855.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137344 restraints weight = 57866.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138159 restraints weight = 48074.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137895 restraints weight = 35822.920| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 32509 Z= 0.104 Angle : 0.569 14.278 44052 Z= 0.291 Chirality : 0.044 0.338 4911 Planarity : 0.004 0.056 5624 Dihedral : 7.672 86.105 4777 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 3.36 % Allowed : 20.77 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.29 (0.13), residues: 4068 helix: 0.54 (0.13), residues: 1786 sheet: -1.63 (0.21), residues: 595 loop : -2.08 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 359 TYR 0.019 0.001 TYR D 307 PHE 0.014 0.001 PHE A 29 TRP 0.025 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00236 (32509) covalent geometry : angle 0.56917 (44052) hydrogen bonds : bond 0.02947 ( 1389) hydrogen bonds : angle 4.44666 ( 4053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 421 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7030 (mm) cc_final: 0.6681 (mt) REVERT: A 97 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7608 (tmmt) REVERT: A 175 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: A 190 ASN cc_start: 0.7295 (t0) cc_final: 0.6932 (t0) REVERT: A 788 ARG cc_start: 0.7911 (ptm160) cc_final: 0.7690 (ptm160) REVERT: A 839 SER cc_start: 0.7112 (OUTLIER) cc_final: 0.6273 (m) REVERT: A 961 ASN cc_start: 0.8603 (m-40) cc_final: 0.8392 (m-40) REVERT: A 1001 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7725 (t) REVERT: A 1035 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.6946 (t0) REVERT: B 25 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6656 (tp) REVERT: B 560 MET cc_start: 0.8676 (mmm) cc_final: 0.8010 (mmm) REVERT: B 565 GLU cc_start: 0.7541 (pm20) cc_final: 0.7221 (pm20) REVERT: B 567 ASP cc_start: 0.7959 (t70) cc_final: 0.7711 (t70) REVERT: B 779 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 973 ILE cc_start: 0.8088 (mm) cc_final: 0.7754 (mm) REVERT: C 94 THR cc_start: 0.6997 (m) cc_final: 0.6746 (p) REVERT: C 391 MET cc_start: 0.8621 (tpp) cc_final: 0.8392 (mmm) REVERT: C 560 MET cc_start: 0.8680 (mmt) cc_final: 0.8021 (mmt) REVERT: C 848 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8435 (pmt-80) REVERT: C 866 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: C 1051 TYR cc_start: 0.8505 (m-80) cc_final: 0.8273 (m-80) REVERT: C 1075 ASP cc_start: 0.8616 (t0) cc_final: 0.8368 (t0) REVERT: D 106 LEU cc_start: 0.3748 (OUTLIER) cc_final: 0.3456 (tp) REVERT: D 242 PHE cc_start: 0.2303 (OUTLIER) cc_final: 0.0626 (t80) REVERT: D 389 ARG cc_start: 0.6520 (ttp80) cc_final: 0.5891 (ttm-80) REVERT: D 1035 ASP cc_start: 0.7327 (t0) cc_final: 0.6976 (t0) REVERT: D 1067 MET cc_start: 0.8119 (mtt) cc_final: 0.7810 (mtm) outliers start: 113 outliers final: 83 residues processed: 508 average time/residue: 0.1817 time to fit residues: 151.8583 Evaluate side-chains 485 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 334 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 348 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS B 27 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144633 restraints weight = 75196.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138862 restraints weight = 77943.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137117 restraints weight = 65030.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137776 restraints weight = 58436.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137783 restraints weight = 41339.205| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32509 Z= 0.136 Angle : 0.591 13.997 44052 Z= 0.302 Chirality : 0.046 0.347 4911 Planarity : 0.004 0.057 5624 Dihedral : 7.367 86.898 4746 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.26 % Favored : 93.72 % Rotamer: Outliers : 3.09 % Allowed : 21.36 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % 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: -1.19 (0.13), residues: 4068 helix: 0.60 (0.13), residues: 1781 sheet: -1.57 (0.21), residues: 595 loop : -2.01 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 561 TYR 0.026 0.001 TYR C 16 PHE 0.012 0.001 PHE B 191 TRP 0.023 0.001 TRP A 49 HIS 0.011 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00324 (32509) covalent geometry : angle 0.59083 (44052) hydrogen bonds : bond 0.03128 ( 1389) hydrogen bonds : angle 4.51450 ( 4053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 388 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7022 (mm) cc_final: 0.6658 (mt) REVERT: A 97 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7609 (tmmt) REVERT: A 175 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: A 190 ASN cc_start: 0.7300 (t0) cc_final: 0.6945 (t0) REVERT: A 788 ARG cc_start: 0.7940 (ptm160) cc_final: 0.7704 (ptm160) REVERT: A 839 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6044 (m) REVERT: A 1001 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7740 (t) REVERT: A 1035 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6926 (t0) REVERT: B 72 VAL cc_start: 0.7450 (t) cc_final: 0.7122 (p) REVERT: B 560 MET cc_start: 0.8689 (mmm) cc_final: 0.8029 (mmm) REVERT: B 565 GLU cc_start: 0.7526 (pm20) cc_final: 0.7236 (pm20) REVERT: B 567 ASP cc_start: 0.7987 (t70) cc_final: 0.7740 (t70) REVERT: B 779 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 973 ILE cc_start: 0.8125 (mm) cc_final: 0.7801 (mm) REVERT: C 326 LEU cc_start: 0.8198 (tp) cc_final: 0.7699 (mt) REVERT: C 848 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8332 (pmt-80) REVERT: C 866 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 1075 ASP cc_start: 0.8568 (t0) cc_final: 0.8313 (t0) REVERT: D 242 PHE cc_start: 0.2218 (OUTLIER) cc_final: 0.0469 (t80) REVERT: D 389 ARG cc_start: 0.6597 (ttp80) cc_final: 0.5948 (ttm-80) REVERT: D 1035 ASP cc_start: 0.7425 (t0) cc_final: 0.7051 (t0) REVERT: D 1050 GLU cc_start: 0.6940 (tt0) cc_final: 0.6679 (mt-10) outliers start: 104 outliers final: 86 residues processed: 470 average time/residue: 0.1896 time to fit residues: 146.0347 Evaluate side-chains 474 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 380 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 5 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 331 optimal weight: 6.9990 chunk 104 optimal weight: 0.0770 chunk 309 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 349 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 overall best weight: 4.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145616 restraints weight = 73046.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138901 restraints weight = 72564.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135263 restraints weight = 65940.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135640 restraints weight = 57552.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135418 restraints weight = 40387.810| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 32509 Z= 0.198 Angle : 0.701 59.197 44052 Z= 0.379 Chirality : 0.048 0.609 4911 Planarity : 0.004 0.056 5624 Dihedral : 7.282 86.924 4737 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 3.06 % Allowed : 21.48 % Favored : 75.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % 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: -1.20 (0.13), residues: 4068 helix: 0.59 (0.13), residues: 1781 sheet: -1.57 (0.21), residues: 595 loop : -2.01 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 28 TYR 0.017 0.002 TYR C 213 PHE 0.014 0.001 PHE B 191 TRP 0.020 0.001 TRP A 49 HIS 0.010 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00472 (32509) covalent geometry : angle 0.70143 (44052) hydrogen bonds : bond 0.03187 ( 1389) hydrogen bonds : angle 4.52257 ( 4053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 379 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7046 (mm) cc_final: 0.6667 (mt) REVERT: A 65 ARG cc_start: 0.6876 (mtt-85) cc_final: 0.6415 (ptt90) REVERT: A 97 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7609 (tmmt) REVERT: A 175 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: A 190 ASN cc_start: 0.7315 (t0) cc_final: 0.6956 (t0) REVERT: A 839 SER cc_start: 0.7235 (OUTLIER) cc_final: 0.6385 (m) REVERT: A 1001 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7728 (t) REVERT: A 1035 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.6922 (t0) REVERT: B 72 VAL cc_start: 0.7402 (t) cc_final: 0.7081 (p) REVERT: B 560 MET cc_start: 0.8671 (mmm) cc_final: 0.8036 (mmm) REVERT: B 565 GLU cc_start: 0.7532 (pm20) cc_final: 0.7259 (pm20) REVERT: B 567 ASP cc_start: 0.7987 (t70) cc_final: 0.7746 (t70) REVERT: B 779 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7879 (mp) REVERT: B 973 ILE cc_start: 0.8113 (mm) cc_final: 0.7800 (mm) REVERT: C 326 LEU cc_start: 0.8128 (tp) cc_final: 0.7681 (mt) REVERT: C 389 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.6939 (ttm-80) REVERT: C 848 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8324 (pmt-80) REVERT: C 866 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: C 1075 ASP cc_start: 0.8657 (t0) cc_final: 0.8397 (t0) REVERT: D 242 PHE cc_start: 0.2197 (OUTLIER) cc_final: 0.0449 (t80) REVERT: D 389 ARG cc_start: 0.6625 (ttp80) cc_final: 0.5969 (ttm-80) REVERT: D 1035 ASP cc_start: 0.7412 (t0) cc_final: 0.7044 (t0) REVERT: D 1050 GLU cc_start: 0.7090 (tt0) cc_final: 0.6715 (mt-10) outliers start: 103 outliers final: 91 residues processed: 460 average time/residue: 0.1940 time to fit residues: 145.8138 Evaluate side-chains 478 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 379 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1054 ILE Chi-restraints excluded: chain D residue 1085 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 235 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 278 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143412 restraints weight = 83849.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140115 restraints weight = 87737.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137593 restraints weight = 48528.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138049 restraints weight = 42436.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139465 restraints weight = 31117.545| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 32509 Z= 0.198 Angle : 0.701 59.197 44052 Z= 0.379 Chirality : 0.048 0.609 4911 Planarity : 0.004 0.056 5624 Dihedral : 7.282 86.924 4737 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 2.94 % Allowed : 21.60 % Favored : 75.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % 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: -1.20 (0.13), residues: 4068 helix: 0.59 (0.13), residues: 1781 sheet: -1.57 (0.21), residues: 595 loop : -2.01 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 28 TYR 0.017 0.002 TYR C 213 PHE 0.014 0.001 PHE B 191 TRP 0.020 0.001 TRP A 49 HIS 0.010 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00472 (32509) covalent geometry : angle 0.70143 (44052) hydrogen bonds : bond 0.03187 ( 1389) hydrogen bonds : angle 4.52257 ( 4053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 379 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.6994 (mm) cc_final: 0.6638 (mt) REVERT: A 65 ARG cc_start: 0.6797 (mtt-85) cc_final: 0.6140 (ptt90) REVERT: A 97 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7599 (tmmt) REVERT: A 175 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: A 190 ASN cc_start: 0.7390 (t0) cc_final: 0.7024 (t0) REVERT: A 839 SER cc_start: 0.6719 (OUTLIER) cc_final: 0.5946 (m) REVERT: A 1001 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7725 (t) REVERT: A 1035 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7031 (t0) REVERT: B 72 VAL cc_start: 0.7655 (t) cc_final: 0.7311 (p) REVERT: B 560 MET cc_start: 0.8547 (mmm) cc_final: 0.7872 (mmm) REVERT: B 565 GLU cc_start: 0.7411 (pm20) cc_final: 0.7094 (pm20) REVERT: B 567 ASP cc_start: 0.7957 (t70) cc_final: 0.7710 (t70) REVERT: B 779 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 973 ILE cc_start: 0.8081 (mm) cc_final: 0.7745 (mm) REVERT: C 326 LEU cc_start: 0.8186 (tp) cc_final: 0.7729 (mt) REVERT: C 389 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6788 (ttm-80) REVERT: C 848 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8290 (pmt-80) REVERT: C 866 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: C 1075 ASP cc_start: 0.8652 (t0) cc_final: 0.8376 (t0) REVERT: D 242 PHE cc_start: 0.2354 (OUTLIER) cc_final: 0.0587 (t80) REVERT: D 389 ARG cc_start: 0.6584 (ttp80) cc_final: 0.5911 (ttm-80) REVERT: D 1035 ASP cc_start: 0.7428 (t0) cc_final: 0.7023 (t0) REVERT: D 1050 GLU cc_start: 0.7007 (tt0) cc_final: 0.6588 (mt-10) outliers start: 99 outliers final: 91 residues processed: 457 average time/residue: 0.2057 time to fit residues: 152.8294 Evaluate side-chains 478 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 379 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1054 ILE Chi-restraints excluded: chain D residue 1085 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 259 optimal weight: 5.9990 chunk 389 optimal weight: 0.9980 chunk 294 optimal weight: 0.2980 chunk 382 optimal weight: 0.2980 chunk 180 optimal weight: 0.0010 chunk 67 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 327 optimal weight: 6.9990 chunk 281 optimal weight: 0.8980 chunk 182 optimal weight: 0.0670 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144262 restraints weight = 77495.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137499 restraints weight = 77805.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135096 restraints weight = 63755.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135740 restraints weight = 56600.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135710 restraints weight = 39151.982| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 32509 Z= 0.198 Angle : 0.701 59.197 44052 Z= 0.379 Chirality : 0.048 0.609 4911 Planarity : 0.004 0.056 5624 Dihedral : 7.282 86.924 4737 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 2.94 % Allowed : 21.60 % Favored : 75.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % 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: -1.20 (0.13), residues: 4068 helix: 0.59 (0.13), residues: 1781 sheet: -1.57 (0.21), residues: 595 loop : -2.01 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 28 TYR 0.017 0.002 TYR C 213 PHE 0.014 0.001 PHE B 191 TRP 0.020 0.001 TRP A 49 HIS 0.010 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00472 (32509) covalent geometry : angle 0.70143 (44052) hydrogen bonds : bond 0.03187 ( 1389) hydrogen bonds : angle 4.52257 ( 4053) =============================================================================== Job complete usr+sys time: 6288.04 seconds wall clock time: 109 minutes 19.06 seconds (6559.06 seconds total)