Starting phenix.real_space_refine on Thu Mar 5 12:34:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6teh_10490/03_2026/6teh_10490.cif Found real_map, /net/cci-nas-00/data/ceres_data/6teh_10490/03_2026/6teh_10490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6teh_10490/03_2026/6teh_10490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6teh_10490/03_2026/6teh_10490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6teh_10490/03_2026/6teh_10490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6teh_10490/03_2026/6teh_10490.map" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 Fe 12 7.16 5 S 54 5.16 5 C 14181 2.51 5 N 4143 2.21 5 O 4245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 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: 22635 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2179 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3246 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2179 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3246 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2179 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3246 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1827 SG CYS C 250 33.585 31.455 90.674 1.00 69.30 S ATOM 9372 SG CYS E 250 100.428 42.631 90.674 1.00 69.30 S ATOM 16917 SG CYS I 250 57.327 94.931 90.674 1.00 69.30 S Time building chain proxies: 4.57, per 1000 atoms: 0.20 Number of scatterers: 22635 At special positions: 0 Unit cell: (122.245, 125.434, 138.19, 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) Fe 12 26.01 S 54 16.00 O 4245 8.00 N 4143 7.00 C 14181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 250 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 150 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 159 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 257 " pdb=" SF4 E 301 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 250 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 150 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 159 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 257 " pdb=" SF4 I 301 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 250 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 150 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 159 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 257 " Number of angles added : 36 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 15.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 83 through 89 removed outlier: 3.699A pdb=" N ALA C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.629A pdb=" N ALA C 136 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA C 137 " --> pdb=" O LEU C 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 137' Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.521A pdb=" N MET C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 17 through 23 removed outlier: 4.167A pdb=" N VAL D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 22 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 17 through 23' Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.579A pdb=" N LEU D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 206 through 211 removed outlier: 3.699A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 765 through 778 removed outlier: 3.701A pdb=" N VAL D 769 " --> pdb=" O PRO D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 813 removed outlier: 3.732A pdb=" N ALA D 808 " --> pdb=" O ALA D 804 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU D 809 " --> pdb=" O GLY D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 842 removed outlier: 3.969A pdb=" N LEU D 842 " --> pdb=" O ALA D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 921 removed outlier: 3.515A pdb=" N GLN D 908 " --> pdb=" O ARG D 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 916 " --> pdb=" O GLY D 912 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 919 " --> pdb=" O LEU D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 934 removed outlier: 3.658A pdb=" N GLY D 934 " --> pdb=" O PRO D 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.576A pdb=" N VAL B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.570A pdb=" N VAL A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 83 through 89 removed outlier: 3.699A pdb=" N ALA E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.629A pdb=" N ALA E 136 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA E 137 " --> pdb=" O LEU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 253 through 261 Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.521A pdb=" N MET E 279 " --> pdb=" O GLY E 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 14 Processing helix chain 'F' and resid 17 through 23 removed outlier: 4.168A pdb=" N VAL F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 17 through 23' Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.579A pdb=" N LEU F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'F' and resid 206 through 211 removed outlier: 3.699A pdb=" N ALA F 211 " --> pdb=" O ALA F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 765 through 778 removed outlier: 3.701A pdb=" N VAL F 769 " --> pdb=" O PRO F 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 813 removed outlier: 3.732A pdb=" N ALA F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU F 809 " --> pdb=" O GLY F 805 " (cutoff:3.500A) Processing helix chain 'F' and resid 838 through 842 removed outlier: 3.969A pdb=" N LEU F 842 " --> pdb=" O ALA F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 903 through 921 removed outlier: 3.515A pdb=" N GLN F 908 " --> pdb=" O ARG F 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 916 " --> pdb=" O GLY F 912 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG F 919 " --> pdb=" O LEU F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 930 through 934 removed outlier: 3.658A pdb=" N GLY F 934 " --> pdb=" O PRO F 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.575A pdb=" N VAL G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.571A pdb=" N VAL H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 83 through 89 removed outlier: 3.699A pdb=" N ALA I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY I 89 " --> pdb=" O ASP I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 137 removed outlier: 3.629A pdb=" N ALA I 136 " --> pdb=" O GLY I 133 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA I 137 " --> pdb=" O LEU I 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 133 through 137' Processing helix chain 'I' and resid 253 through 261 Processing helix chain 'I' and resid 275 through 280 removed outlier: 3.521A pdb=" N MET I 279 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 14 Processing helix chain 'J' and resid 17 through 23 removed outlier: 4.167A pdb=" N VAL J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 17 through 23' Processing helix chain 'J' and resid 41 through 47 removed outlier: 3.578A pdb=" N LEU J 45 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 164 Processing helix chain 'J' and resid 166 through 170 Processing helix chain 'J' and resid 206 through 211 removed outlier: 3.699A pdb=" N ALA J 211 " --> pdb=" O ALA J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 219 Processing helix chain 'J' and resid 765 through 778 removed outlier: 3.700A pdb=" N VAL J 769 " --> pdb=" O PRO J 765 " (cutoff:3.500A) Processing helix chain 'J' and resid 802 through 813 removed outlier: 3.732A pdb=" N ALA J 808 " --> pdb=" O ALA J 804 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU J 809 " --> pdb=" O GLY J 805 " (cutoff:3.500A) Processing helix chain 'J' and resid 838 through 842 removed outlier: 3.969A pdb=" N LEU J 842 " --> pdb=" O ALA J 839 " (cutoff:3.500A) Processing helix chain 'J' and resid 903 through 921 removed outlier: 3.515A pdb=" N GLN J 908 " --> pdb=" O ARG J 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 916 " --> pdb=" O GLY J 912 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG J 919 " --> pdb=" O LEU J 915 " (cutoff:3.500A) Processing helix chain 'J' and resid 930 through 934 removed outlier: 3.658A pdb=" N GLY J 934 " --> pdb=" O PRO J 931 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 removed outlier: 3.576A pdb=" N VAL K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG K 61 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 68 removed outlier: 3.570A pdb=" N VAL L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG L 61 " --> pdb=" O ASP L 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA L 64 " --> pdb=" O GLU L 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'C' and resid 15 through 16 removed outlier: 3.589A pdb=" N THR C 16 " --> pdb=" O ARG A 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=3, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.672A pdb=" N PHE C 127 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'C' and resid 227 through 230 removed outlier: 6.649A pdb=" N LEU C 227 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 218 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'D' and resid 74 through 76 Processing sheet with id=6, first strand: chain 'D' and resid 79 through 81 removed outlier: 3.843A pdb=" N GLU D 199 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG D 131 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.551A pdb=" N ALA D 177 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=9, first strand: chain 'D' and resid 851 through 855 removed outlier: 3.622A pdb=" N ALA D 925 " --> pdb=" O ALA D 968 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN D 965 " --> pdb=" O VAL D 958 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D 958 " --> pdb=" O GLN D 965 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 882 through 884 removed outlier: 6.318A pdb=" N ARG D 864 " --> pdb=" O ALA D 894 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.609A pdb=" N GLU B 25 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 37 " --> pdb=" O GLU B 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.942A pdb=" N GLY B 52 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 200 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 54 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=14, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY A 52 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 200 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 54 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'A' and resid 158 through 159 Processing sheet with id=16, first strand: chain 'E' and resid 15 through 16 removed outlier: 3.589A pdb=" N THR E 16 " --> pdb=" O ARG H 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=16 Processing sheet with id=17, first strand: chain 'E' and resid 31 through 35 Processing sheet with id=18, first strand: chain 'E' and resid 74 through 75 removed outlier: 3.671A pdb=" N PHE E 127 " --> pdb=" O GLY E 74 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 227 through 230 removed outlier: 6.649A pdb=" N LEU E 227 " --> pdb=" O ASP E 218 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP E 218 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=21, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.843A pdb=" N GLU F 199 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG F 131 " --> pdb=" O GLU F 199 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.550A pdb=" N ALA F 177 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=24, first strand: chain 'F' and resid 851 through 855 removed outlier: 3.622A pdb=" N ALA F 925 " --> pdb=" O ALA F 968 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN F 965 " --> pdb=" O VAL F 958 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL F 958 " --> pdb=" O GLN F 965 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'F' and resid 882 through 884 removed outlier: 6.317A pdb=" N ARG F 864 " --> pdb=" O ALA F 894 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.609A pdb=" N GLU G 25 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 37 " --> pdb=" O GLU G 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=26 Processing sheet with id=27, first strand: chain 'G' and resid 52 through 54 removed outlier: 3.942A pdb=" N GLY G 52 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 200 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG G 54 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 158 through 159 Processing sheet with id=29, first strand: chain 'H' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY H 52 " --> pdb=" O LEU H 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU H 200 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 54 " --> pdb=" O GLY H 198 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 158 through 159 Processing sheet with id=31, first strand: chain 'I' and resid 15 through 16 removed outlier: 3.589A pdb=" N THR I 16 " --> pdb=" O ARG L 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=31 Processing sheet with id=32, first strand: chain 'I' and resid 31 through 35 Processing sheet with id=33, first strand: chain 'I' and resid 74 through 75 removed outlier: 3.672A pdb=" N PHE I 127 " --> pdb=" O GLY I 74 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 227 through 230 removed outlier: 6.649A pdb=" N LEU I 227 " --> pdb=" O ASP I 218 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP I 218 " --> pdb=" O LEU I 227 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=36, first strand: chain 'J' and resid 79 through 81 removed outlier: 3.843A pdb=" N GLU J 199 " --> pdb=" O ARG J 131 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG J 131 " --> pdb=" O GLU J 199 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'J' and resid 84 through 85 removed outlier: 6.550A pdb=" N ALA J 177 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=39, first strand: chain 'J' and resid 851 through 855 removed outlier: 3.622A pdb=" N ALA J 925 " --> pdb=" O ALA J 968 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN J 965 " --> pdb=" O VAL J 958 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL J 958 " --> pdb=" O GLN J 965 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'J' and resid 882 through 884 removed outlier: 6.318A pdb=" N ARG J 864 " --> pdb=" O ALA J 894 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.609A pdb=" N GLU K 25 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN K 37 " --> pdb=" O GLU K 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=41 Processing sheet with id=42, first strand: chain 'K' and resid 52 through 54 removed outlier: 3.943A pdb=" N GLY K 52 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU K 200 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG K 54 " --> pdb=" O GLY K 198 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA K 197 " --> pdb=" O GLN K 193 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'K' and resid 158 through 159 Processing sheet with id=44, first strand: chain 'L' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY L 52 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 200 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG L 54 " --> pdb=" O GLY L 198 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'L' and resid 158 through 159 378 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10006 1.43 - 1.64: 12980 1.64 - 1.85: 66 1.85 - 2.06: 0 2.06 - 2.27: 36 Bond restraints: 23088 Sorted by residual: bond pdb=" N ILE F 782 " pdb=" CA ILE F 782 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.27e-02 6.20e+03 1.12e+01 bond pdb=" N ILE J 782 " pdb=" CA ILE J 782 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.27e-02 6.20e+03 1.11e+01 bond pdb=" N ILE D 782 " pdb=" CA ILE D 782 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.27e-02 6.20e+03 1.08e+01 bond pdb=" C ILE F 225 " pdb=" N PRO F 226 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 1.00e+01 bond pdb=" C ILE D 225 " pdb=" N PRO D 226 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 9.90e+00 ... (remaining 23083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 30452 3.21 - 6.41: 758 6.41 - 9.62: 80 9.62 - 12.82: 18 12.82 - 16.03: 3 Bond angle restraints: 31311 Sorted by residual: angle pdb=" C ILE D 225 " pdb=" N PRO D 226 " pdb=" CA PRO D 226 " ideal model delta sigma weight residual 119.05 125.47 -6.42 1.11e+00 8.12e-01 3.35e+01 angle pdb=" C ILE F 225 " pdb=" N PRO F 226 " pdb=" CA PRO F 226 " ideal model delta sigma weight residual 119.05 125.45 -6.40 1.11e+00 8.12e-01 3.33e+01 angle pdb=" C ILE J 225 " pdb=" N PRO J 226 " pdb=" CA PRO J 226 " ideal model delta sigma weight residual 119.05 125.45 -6.40 1.11e+00 8.12e-01 3.32e+01 angle pdb=" C PRO D 159 " pdb=" N LYS D 160 " pdb=" CA LYS D 160 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C PRO F 159 " pdb=" N LYS F 160 " pdb=" CA LYS F 160 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 ... (remaining 31306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 11984 14.52 - 29.03: 1183 29.03 - 43.54: 297 43.54 - 58.06: 21 58.06 - 72.57: 15 Dihedral angle restraints: 13500 sinusoidal: 5214 harmonic: 8286 Sorted by residual: dihedral pdb=" CA LEU J 215 " pdb=" C LEU J 215 " pdb=" N THR J 216 " pdb=" CA THR J 216 " ideal model delta harmonic sigma weight residual -180.00 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU D 215 " pdb=" C LEU D 215 " pdb=" N THR D 216 " pdb=" CA THR D 216 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LEU F 215 " pdb=" C LEU F 215 " pdb=" N THR F 216 " pdb=" CA THR F 216 " ideal model delta harmonic sigma weight residual 180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 13497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2358 0.063 - 0.127: 802 0.127 - 0.190: 191 0.190 - 0.253: 51 0.253 - 0.316: 6 Chirality restraints: 3408 Sorted by residual: chirality pdb=" CB ILE C 273 " pdb=" CA ILE C 273 " pdb=" CG1 ILE C 273 " pdb=" CG2 ILE C 273 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE E 273 " pdb=" CA ILE E 273 " pdb=" CG1 ILE E 273 " pdb=" CG2 ILE E 273 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE I 273 " pdb=" CA ILE I 273 " pdb=" CG1 ILE I 273 " pdb=" CG2 ILE I 273 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 3405 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO K 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO K 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 166 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO G 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " 0.046 5.00e-02 4.00e+02 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4727 2.77 - 3.30: 21792 3.30 - 3.84: 37392 3.84 - 4.37: 42842 4.37 - 4.90: 72126 Nonbonded interactions: 178879 Sorted by model distance: nonbonded pdb=" O LEU E 18 " pdb=" ND2 ASN H 37 " model vdw 2.239 3.120 nonbonded pdb=" O LEU C 18 " pdb=" ND2 ASN A 37 " model vdw 2.239 3.120 nonbonded pdb=" O LEU I 18 " pdb=" ND2 ASN L 37 " model vdw 2.240 3.120 nonbonded pdb=" OE2 GLU A 34 " pdb=" NH1 ARG G 182 " model vdw 2.286 3.120 nonbonded pdb=" OE2 GLU H 34 " pdb=" NH1 ARG K 182 " model vdw 2.286 3.120 ... (remaining 178874 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.020 0.877 23100 Z= 0.706 Angle : 1.647 56.847 31347 Z= 0.719 Chirality : 0.069 0.316 3408 Planarity : 0.008 0.083 4188 Dihedral : 12.443 72.574 8238 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.81 % Favored : 84.98 % Rotamer: Outliers : 1.08 % Allowed : 11.04 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.12), residues: 2943 helix: -4.31 (0.13), residues: 351 sheet: -2.81 (0.18), residues: 627 loop : -3.55 (0.11), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 122 TYR 0.018 0.003 TYR F 178 PHE 0.029 0.003 PHE H 76 TRP 0.037 0.004 TRP I 22 HIS 0.011 0.002 HIS I 272 Details of bonding type rmsd covalent geometry : bond 0.00916 (23088) covalent geometry : angle 1.23572 (31311) hydrogen bonds : bond 0.31559 ( 378) hydrogen bonds : angle 11.64378 ( 927) metal coordination : bond 0.80011 ( 12) metal coordination : angle 32.14791 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 690 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8653 (tm-30) REVERT: D 135 ASP cc_start: 0.7417 (t0) cc_final: 0.7045 (t0) REVERT: D 228 THR cc_start: 0.7844 (m) cc_final: 0.7579 (t) REVERT: D 853 THR cc_start: 0.9414 (m) cc_final: 0.8826 (p) REVERT: B 38 SER cc_start: 0.8824 (t) cc_final: 0.8533 (m) REVERT: B 58 ASP cc_start: 0.8955 (t0) cc_final: 0.8715 (t70) REVERT: A 58 ASP cc_start: 0.6083 (t0) cc_final: 0.5203 (t0) REVERT: A 73 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6470 (pp) REVERT: A 76 PHE cc_start: 0.8537 (p90) cc_final: 0.7928 (p90) REVERT: E 61 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8439 (mm-40) REVERT: E 83 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8401 (tm-30) REVERT: E 99 TRP cc_start: 0.8828 (m100) cc_final: 0.8315 (m100) REVERT: F 74 ARG cc_start: 0.8705 (ptp-110) cc_final: 0.8499 (mtp-110) REVERT: F 135 ASP cc_start: 0.7312 (t0) cc_final: 0.6985 (t0) REVERT: F 220 ARG cc_start: 0.7646 (tpt170) cc_final: 0.7412 (tmt170) REVERT: F 762 VAL cc_start: 0.9171 (t) cc_final: 0.8970 (p) REVERT: F 853 THR cc_start: 0.9406 (m) cc_final: 0.8791 (p) REVERT: G 38 SER cc_start: 0.8937 (t) cc_final: 0.8703 (m) REVERT: G 208 VAL cc_start: 0.7731 (t) cc_final: 0.7257 (t) REVERT: H 58 ASP cc_start: 0.6260 (t0) cc_final: 0.5528 (t0) REVERT: H 73 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6213 (pp) REVERT: H 178 ASP cc_start: 0.6184 (t0) cc_final: 0.5691 (t0) REVERT: I 54 MET cc_start: 0.6808 (mmm) cc_final: 0.6589 (mmm) REVERT: I 65 LEU cc_start: 0.8947 (mt) cc_final: 0.8744 (mm) REVERT: I 83 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8621 (tm-30) REVERT: J 135 ASP cc_start: 0.7403 (t0) cc_final: 0.7090 (t0) REVERT: J 220 ARG cc_start: 0.7555 (tpt170) cc_final: 0.7323 (tmt170) REVERT: J 768 SER cc_start: 0.8937 (p) cc_final: 0.8673 (t) REVERT: J 871 GLU cc_start: 0.7909 (tt0) cc_final: 0.7272 (tt0) REVERT: K 38 SER cc_start: 0.8887 (t) cc_final: 0.8588 (m) REVERT: K 58 ASP cc_start: 0.8936 (t0) cc_final: 0.8372 (t70) REVERT: L 58 ASP cc_start: 0.6040 (t0) cc_final: 0.5166 (t0) REVERT: L 73 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6303 (pp) outliers start: 24 outliers final: 3 residues processed: 708 average time/residue: 0.1728 time to fit residues: 181.9790 Evaluate side-chains 424 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 418 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN B 4 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS A 72 GLN A 74 HIS ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN G 4 HIS ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS H 72 GLN I 142 GLN ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN K 4 HIS ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS L 72 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093907 restraints weight = 53856.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096262 restraints weight = 28525.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097927 restraints weight = 17681.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098960 restraints weight = 11818.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099710 restraints weight = 8675.311| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23100 Z= 0.152 Angle : 0.832 21.479 31347 Z= 0.397 Chirality : 0.047 0.209 3408 Planarity : 0.007 0.072 4188 Dihedral : 7.167 54.543 3305 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 5.18 % Allowed : 16.35 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.12), residues: 2943 helix: -3.29 (0.16), residues: 381 sheet: -2.62 (0.19), residues: 546 loop : -3.02 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 182 TYR 0.017 0.001 TYR I 73 PHE 0.044 0.002 PHE K 76 TRP 0.026 0.002 TRP C 22 HIS 0.008 0.001 HIS L 74 Details of bonding type rmsd covalent geometry : bond 0.00321 (23088) covalent geometry : angle 0.75008 (31311) hydrogen bonds : bond 0.04918 ( 378) hydrogen bonds : angle 7.97455 ( 927) metal coordination : bond 0.02018 ( 12) metal coordination : angle 10.64623 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 536 time to evaluate : 0.608 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: C 22 TRP cc_start: 0.8958 (p90) cc_final: 0.8092 (p90) REVERT: C 69 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8329 (m110) REVERT: C 279 MET cc_start: 0.9402 (tpt) cc_final: 0.9067 (tpt) REVERT: D 135 ASP cc_start: 0.7394 (t0) cc_final: 0.7126 (t0) REVERT: D 178 TYR cc_start: 0.9043 (p90) cc_final: 0.8278 (p90) REVERT: D 220 ARG cc_start: 0.4347 (tmt170) cc_final: 0.4014 (tmt170) REVERT: D 745 TRP cc_start: 0.6141 (p-90) cc_final: 0.5160 (p-90) REVERT: D 841 ASP cc_start: 0.7436 (t0) cc_final: 0.7138 (t0) REVERT: D 853 THR cc_start: 0.9239 (m) cc_final: 0.8605 (p) REVERT: D 871 GLU cc_start: 0.7889 (tt0) cc_final: 0.7550 (tt0) REVERT: B 38 SER cc_start: 0.8841 (t) cc_final: 0.8482 (m) REVERT: B 58 ASP cc_start: 0.8284 (t0) cc_final: 0.8056 (t70) REVERT: B 59 VAL cc_start: 0.9418 (t) cc_final: 0.9063 (p) REVERT: B 63 ILE cc_start: 0.9368 (pp) cc_final: 0.8787 (mt) REVERT: B 76 PHE cc_start: 0.8788 (p90) cc_final: 0.8559 (p90) REVERT: A 8 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: A 34 GLU cc_start: 0.7470 (pt0) cc_final: 0.7258 (pt0) REVERT: A 76 PHE cc_start: 0.8374 (p90) cc_final: 0.7967 (p90) REVERT: E 170 LEU cc_start: 0.9391 (tm) cc_final: 0.9180 (tm) REVERT: E 237 ASN cc_start: 0.8384 (m-40) cc_final: 0.7911 (t0) REVERT: F 745 TRP cc_start: 0.6367 (p-90) cc_final: 0.5408 (p-90) REVERT: F 762 VAL cc_start: 0.8927 (t) cc_final: 0.8705 (p) REVERT: F 781 GLU cc_start: 0.7132 (tp30) cc_final: 0.6926 (tm-30) REVERT: F 794 TYR cc_start: 0.8937 (t80) cc_final: 0.8602 (t80) REVERT: F 823 GLN cc_start: 0.7543 (mp10) cc_final: 0.6269 (mt0) REVERT: F 832 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7697 (mtm110) REVERT: F 841 ASP cc_start: 0.7566 (t0) cc_final: 0.7060 (t0) REVERT: F 853 THR cc_start: 0.9202 (m) cc_final: 0.8529 (p) REVERT: G 59 VAL cc_start: 0.9272 (t) cc_final: 0.9021 (p) REVERT: G 76 PHE cc_start: 0.8786 (p90) cc_final: 0.8558 (p90) REVERT: G 208 VAL cc_start: 0.8465 (t) cc_final: 0.8206 (t) REVERT: H 8 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: H 76 PHE cc_start: 0.8347 (p90) cc_final: 0.8120 (p90) REVERT: H 194 SER cc_start: 0.8445 (t) cc_final: 0.7526 (m) REVERT: I 194 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8272 (ttm-80) REVERT: J 79 MET cc_start: 0.8827 (tpt) cc_final: 0.8413 (tpt) REVERT: J 135 ASP cc_start: 0.7216 (t0) cc_final: 0.6860 (t0) REVERT: J 178 TYR cc_start: 0.9001 (p90) cc_final: 0.8157 (p90) REVERT: J 823 GLN cc_start: 0.7773 (mp10) cc_final: 0.6890 (mt0) REVERT: J 841 ASP cc_start: 0.7682 (t0) cc_final: 0.7340 (t0) REVERT: J 853 THR cc_start: 0.9220 (m) cc_final: 0.8667 (p) REVERT: J 871 GLU cc_start: 0.7792 (tt0) cc_final: 0.7321 (tt0) REVERT: J 879 LYS cc_start: 0.8529 (mttt) cc_final: 0.8226 (mttt) REVERT: K 38 SER cc_start: 0.8639 (t) cc_final: 0.8399 (m) REVERT: K 58 ASP cc_start: 0.7853 (t0) cc_final: 0.7526 (t70) REVERT: K 59 VAL cc_start: 0.9329 (t) cc_final: 0.8925 (p) REVERT: K 63 ILE cc_start: 0.9332 (pp) cc_final: 0.8739 (mt) REVERT: K 76 PHE cc_start: 0.8615 (p90) cc_final: 0.8387 (p90) REVERT: K 202 GLN cc_start: 0.7495 (mp10) cc_final: 0.7224 (mp10) REVERT: L 194 SER cc_start: 0.8459 (t) cc_final: 0.7584 (m) outliers start: 115 outliers final: 54 residues processed: 613 average time/residue: 0.1456 time to fit residues: 140.6710 Evaluate side-chains 475 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 418 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 171 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 289 ASN J 764 GLN K 4 HIS ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083931 restraints weight = 56377.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.086152 restraints weight = 30580.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087638 restraints weight = 19170.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088640 restraints weight = 13175.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089362 restraints weight = 9868.487| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23100 Z= 0.288 Angle : 0.920 21.237 31347 Z= 0.441 Chirality : 0.051 0.247 3408 Planarity : 0.007 0.072 4188 Dihedral : 7.143 56.580 3300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 6.85 % Allowed : 17.52 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.95 (0.13), residues: 2943 helix: -2.21 (0.23), residues: 381 sheet: -2.21 (0.21), residues: 462 loop : -3.03 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 69 TYR 0.023 0.002 TYR B 47 PHE 0.052 0.003 PHE L 76 TRP 0.027 0.003 TRP J 87 HIS 0.008 0.002 HIS L 74 Details of bonding type rmsd covalent geometry : bond 0.00638 (23088) covalent geometry : angle 0.84709 (31311) hydrogen bonds : bond 0.04390 ( 378) hydrogen bonds : angle 7.50552 ( 927) metal coordination : bond 0.02978 ( 12) metal coordination : angle 10.61981 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 431 time to evaluate : 0.715 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: C 279 MET cc_start: 0.9299 (tpt) cc_final: 0.8984 (tpt) REVERT: D 54 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: D 135 ASP cc_start: 0.7649 (t0) cc_final: 0.7287 (t0) REVERT: D 189 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8265 (p90) REVERT: D 220 ARG cc_start: 0.4905 (tmt170) cc_final: 0.4669 (tmt170) REVERT: D 841 ASP cc_start: 0.7748 (t0) cc_final: 0.7479 (t0) REVERT: D 853 THR cc_start: 0.9275 (m) cc_final: 0.8714 (p) REVERT: D 871 GLU cc_start: 0.8065 (tt0) cc_final: 0.7852 (tt0) REVERT: D 938 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9146 (p) REVERT: B 35 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 38 SER cc_start: 0.8899 (t) cc_final: 0.8608 (m) REVERT: B 184 ASP cc_start: 0.7990 (t0) cc_final: 0.7601 (t70) REVERT: E 194 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8136 (ttm170) REVERT: E 196 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7442 (p90) REVERT: F 841 ASP cc_start: 0.7831 (t0) cc_final: 0.7480 (t0) REVERT: F 853 THR cc_start: 0.9335 (m) cc_final: 0.8684 (p) REVERT: G 77 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8091 (ptm160) REVERT: G 184 ASP cc_start: 0.8086 (t0) cc_final: 0.7591 (t0) REVERT: H 48 ASP cc_start: 0.8478 (m-30) cc_final: 0.8219 (m-30) REVERT: H 178 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7524 (t70) REVERT: H 194 SER cc_start: 0.8428 (t) cc_final: 0.7571 (m) REVERT: J 79 MET cc_start: 0.8731 (tpt) cc_final: 0.8376 (tpt) REVERT: J 794 TYR cc_start: 0.9024 (t80) cc_final: 0.8793 (t80) REVERT: J 841 ASP cc_start: 0.7789 (t0) cc_final: 0.7545 (t0) REVERT: J 853 THR cc_start: 0.9322 (m) cc_final: 0.8841 (p) REVERT: J 871 GLU cc_start: 0.7946 (tt0) cc_final: 0.6974 (tt0) REVERT: J 879 LYS cc_start: 0.8826 (mttt) cc_final: 0.7481 (mttt) REVERT: K 38 SER cc_start: 0.8717 (t) cc_final: 0.8493 (m) REVERT: K 184 ASP cc_start: 0.8115 (t0) cc_final: 0.7685 (t70) REVERT: L 54 ARG cc_start: 0.6778 (mtt180) cc_final: 0.6428 (mtt-85) REVERT: L 69 ARG cc_start: 0.7196 (pmm150) cc_final: 0.6473 (pmm150) REVERT: L 194 SER cc_start: 0.8440 (t) cc_final: 0.7651 (m) outliers start: 152 outliers final: 105 residues processed: 539 average time/residue: 0.1509 time to fit residues: 127.2608 Evaluate side-chains 472 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 361 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 875 ASP Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 801 THR Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 77 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 224 optimal weight: 9.9990 chunk 142 optimal weight: 0.0370 chunk 133 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 166 optimal weight: 8.9990 chunk 280 optimal weight: 0.7980 chunk 262 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** I 266 ASN ** 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 = 0.3293 r_free = 0.3293 target = 0.101040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090596 restraints weight = 54559.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092869 restraints weight = 29883.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094342 restraints weight = 18687.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095379 restraints weight = 12796.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096119 restraints weight = 9491.572| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23100 Z= 0.137 Angle : 0.771 16.266 31347 Z= 0.375 Chirality : 0.047 0.272 3408 Planarity : 0.006 0.064 4188 Dihedral : 6.431 59.813 3300 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 5.59 % Allowed : 21.49 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.13), residues: 2943 helix: -1.60 (0.25), residues: 381 sheet: -2.12 (0.20), residues: 555 loop : -2.76 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 147 TYR 0.023 0.001 TYR E 73 PHE 0.039 0.002 PHE L 76 TRP 0.031 0.002 TRP J 87 HIS 0.007 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00294 (23088) covalent geometry : angle 0.72909 (31311) hydrogen bonds : bond 0.03457 ( 378) hydrogen bonds : angle 7.04513 ( 927) metal coordination : bond 0.01096 ( 12) metal coordination : angle 7.44867 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 439 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8698 (p90) cc_final: 0.8287 (p90) REVERT: C 65 LEU cc_start: 0.9088 (mm) cc_final: 0.8812 (mm) REVERT: C 145 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 279 MET cc_start: 0.9112 (tpt) cc_final: 0.8844 (tpt) REVERT: D 54 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: D 220 ARG cc_start: 0.4856 (OUTLIER) cc_final: 0.4493 (tmt170) REVERT: D 841 ASP cc_start: 0.7471 (t0) cc_final: 0.7240 (t0) REVERT: D 853 THR cc_start: 0.9190 (m) cc_final: 0.8651 (p) REVERT: B 178 ASP cc_start: 0.8061 (t0) cc_final: 0.6730 (t0) REVERT: B 184 ASP cc_start: 0.7687 (t0) cc_final: 0.7434 (t70) REVERT: A 48 ASP cc_start: 0.8257 (m-30) cc_final: 0.7904 (m-30) REVERT: E 54 MET cc_start: 0.6180 (mmt) cc_final: 0.5516 (mmp) REVERT: E 194 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8452 (ttm170) REVERT: E 196 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7179 (p90) REVERT: F 781 GLU cc_start: 0.7505 (tp30) cc_final: 0.7103 (tm-30) REVERT: F 841 ASP cc_start: 0.7578 (t0) cc_final: 0.7366 (t0) REVERT: F 853 THR cc_start: 0.9197 (m) cc_final: 0.8521 (p) REVERT: F 871 GLU cc_start: 0.7872 (tt0) cc_final: 0.7112 (tt0) REVERT: G 4 HIS cc_start: 0.6383 (t70) cc_final: 0.5968 (t-170) REVERT: G 77 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7865 (ptm160) REVERT: G 184 ASP cc_start: 0.7802 (t0) cc_final: 0.7502 (t70) REVERT: H 178 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7390 (t70) REVERT: J 135 ASP cc_start: 0.7483 (t0) cc_final: 0.7244 (t0) REVERT: J 841 ASP cc_start: 0.7669 (t0) cc_final: 0.7433 (t0) REVERT: J 853 THR cc_start: 0.9238 (m) cc_final: 0.8773 (p) REVERT: J 871 GLU cc_start: 0.7807 (tt0) cc_final: 0.7081 (tt0) REVERT: K 184 ASP cc_start: 0.7863 (t0) cc_final: 0.7550 (t70) outliers start: 124 outliers final: 77 residues processed: 522 average time/residue: 0.1488 time to fit residues: 122.0452 Evaluate side-chains 458 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 375 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 811 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 114 optimal weight: 0.0070 chunk 30 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 126 optimal weight: 0.0870 chunk 267 optimal weight: 1.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 289 ASN ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.087608 restraints weight = 55138.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089875 restraints weight = 29722.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.091471 restraints weight = 18563.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092479 restraints weight = 12536.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093238 restraints weight = 9285.080| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23100 Z= 0.189 Angle : 0.793 17.465 31347 Z= 0.380 Chirality : 0.048 0.302 3408 Planarity : 0.006 0.062 4188 Dihedral : 6.365 57.317 3300 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 6.49 % Allowed : 21.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.14), residues: 2943 helix: -1.39 (0.26), residues: 381 sheet: -2.06 (0.22), residues: 477 loop : -2.70 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.018 0.002 TYR J 794 PHE 0.035 0.002 PHE L 76 TRP 0.032 0.002 TRP J 87 HIS 0.010 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00417 (23088) covalent geometry : angle 0.73858 (31311) hydrogen bonds : bond 0.03380 ( 378) hydrogen bonds : angle 6.91212 ( 927) metal coordination : bond 0.01620 ( 12) metal coordination : angle 8.51155 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 393 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8688 (p90) cc_final: 0.8278 (p90) REVERT: C 65 LEU cc_start: 0.9240 (mm) cc_final: 0.8975 (mm) REVERT: C 279 MET cc_start: 0.9204 (tpt) cc_final: 0.8912 (tpt) REVERT: D 54 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: D 841 ASP cc_start: 0.7677 (t0) cc_final: 0.7420 (t0) REVERT: D 853 THR cc_start: 0.9200 (m) cc_final: 0.8670 (p) REVERT: D 871 GLU cc_start: 0.8050 (tt0) cc_final: 0.7826 (tt0) REVERT: B 60 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7742 (pt0) REVERT: B 178 ASP cc_start: 0.8181 (t0) cc_final: 0.6822 (t0) REVERT: B 184 ASP cc_start: 0.7766 (t0) cc_final: 0.7522 (t70) REVERT: E 54 MET cc_start: 0.6161 (mmt) cc_final: 0.5609 (mmp) REVERT: E 196 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7289 (p90) REVERT: F 75 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9058 (pt) REVERT: F 841 ASP cc_start: 0.7813 (t0) cc_final: 0.7579 (t0) REVERT: F 853 THR cc_start: 0.9209 (m) cc_final: 0.8508 (p) REVERT: F 871 GLU cc_start: 0.7954 (tt0) cc_final: 0.7567 (tt0) REVERT: G 4 HIS cc_start: 0.6287 (t70) cc_final: 0.6044 (t-170) REVERT: G 184 ASP cc_start: 0.7869 (t0) cc_final: 0.7551 (t70) REVERT: H 48 ASP cc_start: 0.8130 (m-30) cc_final: 0.7914 (m-30) REVERT: H 158 ILE cc_start: 0.8519 (mp) cc_final: 0.8132 (tt) REVERT: H 178 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7388 (t70) REVERT: J 135 ASP cc_start: 0.7560 (t0) cc_final: 0.7165 (t0) REVERT: J 145 ASN cc_start: 0.8694 (t0) cc_final: 0.8117 (t0) REVERT: J 182 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6402 (mt-10) REVERT: J 841 ASP cc_start: 0.7833 (t0) cc_final: 0.7601 (t0) REVERT: J 853 THR cc_start: 0.9268 (m) cc_final: 0.8809 (p) REVERT: J 871 GLU cc_start: 0.7765 (tt0) cc_final: 0.7481 (tt0) REVERT: K 4 HIS cc_start: 0.5659 (t70) cc_final: 0.5268 (t-170) REVERT: K 158 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8085 (mp) REVERT: K 184 ASP cc_start: 0.7924 (t0) cc_final: 0.7608 (t70) REVERT: L 21 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8188 (mt-10) REVERT: L 158 ILE cc_start: 0.8813 (mm) cc_final: 0.8451 (tp) outliers start: 144 outliers final: 110 residues processed: 497 average time/residue: 0.1495 time to fit residues: 116.5583 Evaluate side-chains 470 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 355 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 801 THR Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 0.0050 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN I 10 HIS I 140 GLN ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.087416 restraints weight = 55513.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089656 restraints weight = 29983.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091237 restraints weight = 18965.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.092239 restraints weight = 13032.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093009 restraints weight = 9710.406| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23100 Z= 0.182 Angle : 0.787 16.569 31347 Z= 0.379 Chirality : 0.048 0.317 3408 Planarity : 0.005 0.059 4188 Dihedral : 6.324 54.340 3300 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 6.58 % Allowed : 22.84 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.14), residues: 2943 helix: -1.20 (0.27), residues: 363 sheet: -1.95 (0.22), residues: 480 loop : -2.67 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 69 TYR 0.022 0.002 TYR I 73 PHE 0.036 0.002 PHE G 76 TRP 0.036 0.002 TRP J 87 HIS 0.009 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00408 (23088) covalent geometry : angle 0.73593 (31311) hydrogen bonds : bond 0.03254 ( 378) hydrogen bonds : angle 6.88827 ( 927) metal coordination : bond 0.01670 ( 12) metal coordination : angle 8.26902 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 403 time to evaluate : 0.811 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: C 22 TRP cc_start: 0.8615 (p90) cc_final: 0.8273 (p90) REVERT: C 65 LEU cc_start: 0.9268 (mm) cc_final: 0.9007 (mm) REVERT: C 279 MET cc_start: 0.9235 (tpt) cc_final: 0.8922 (tpt) REVERT: D 54 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: D 841 ASP cc_start: 0.7730 (t0) cc_final: 0.7479 (t0) REVERT: D 853 THR cc_start: 0.9206 (m) cc_final: 0.8675 (p) REVERT: B 60 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7690 (pt0) REVERT: B 178 ASP cc_start: 0.8201 (t0) cc_final: 0.6916 (t0) REVERT: B 184 ASP cc_start: 0.7800 (t0) cc_final: 0.7580 (t70) REVERT: E 196 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7222 (p90) REVERT: F 6 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8167 (tp) REVERT: F 75 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9002 (pt) REVERT: F 841 ASP cc_start: 0.7839 (t0) cc_final: 0.7601 (t0) REVERT: F 853 THR cc_start: 0.9235 (m) cc_final: 0.8601 (p) REVERT: G 60 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7776 (pt0) REVERT: G 184 ASP cc_start: 0.7840 (t0) cc_final: 0.7576 (t70) REVERT: H 25 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: H 67 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6746 (tm-30) REVERT: H 158 ILE cc_start: 0.8870 (mp) cc_final: 0.8580 (tt) REVERT: H 178 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7232 (t70) REVERT: I 229 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7199 (mm-30) REVERT: J 135 ASP cc_start: 0.7602 (t0) cc_final: 0.7241 (t0) REVERT: J 145 ASN cc_start: 0.8653 (t0) cc_final: 0.8037 (t0) REVERT: J 182 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6372 (mt-10) REVERT: J 841 ASP cc_start: 0.7827 (t0) cc_final: 0.7610 (t0) REVERT: J 853 THR cc_start: 0.9262 (m) cc_final: 0.8780 (p) REVERT: J 871 GLU cc_start: 0.7791 (tt0) cc_final: 0.7287 (tt0) REVERT: K 60 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7807 (pt0) REVERT: K 158 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8174 (mp) REVERT: K 178 ASP cc_start: 0.8214 (t0) cc_final: 0.6922 (t0) REVERT: K 184 ASP cc_start: 0.7938 (t0) cc_final: 0.7597 (t0) REVERT: L 158 ILE cc_start: 0.8891 (mm) cc_final: 0.8545 (tp) outliers start: 146 outliers final: 117 residues processed: 509 average time/residue: 0.1465 time to fit residues: 118.6309 Evaluate side-chains 490 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 366 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 195 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 292 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 171 optimal weight: 0.0010 chunk 274 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 2.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 72 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 193 GLN ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.085745 restraints weight = 55779.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.088050 restraints weight = 29767.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089636 restraints weight = 18818.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090726 restraints weight = 12897.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.091529 restraints weight = 9504.909| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23100 Z= 0.209 Angle : 0.819 17.295 31347 Z= 0.392 Chirality : 0.049 0.338 3408 Planarity : 0.006 0.059 4188 Dihedral : 6.403 51.346 3300 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 6.89 % Allowed : 23.92 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.14), residues: 2943 helix: -1.14 (0.28), residues: 360 sheet: -1.98 (0.22), residues: 486 loop : -2.67 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 69 TYR 0.019 0.002 TYR J 794 PHE 0.051 0.002 PHE L 76 TRP 0.041 0.002 TRP J 87 HIS 0.010 0.002 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00470 (23088) covalent geometry : angle 0.76038 (31311) hydrogen bonds : bond 0.03286 ( 378) hydrogen bonds : angle 6.89603 ( 927) metal coordination : bond 0.02017 ( 12) metal coordination : angle 8.97995 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 382 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8647 (p90) cc_final: 0.8282 (p90) REVERT: C 65 LEU cc_start: 0.9282 (mm) cc_final: 0.9032 (mm) REVERT: C 279 MET cc_start: 0.9259 (tpt) cc_final: 0.8942 (tpt) REVERT: D 54 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: D 853 THR cc_start: 0.9220 (m) cc_final: 0.8680 (p) REVERT: B 60 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7698 (pt0) REVERT: B 178 ASP cc_start: 0.8207 (t0) cc_final: 0.6909 (t0) REVERT: B 184 ASP cc_start: 0.7895 (t0) cc_final: 0.7657 (t70) REVERT: A 54 ARG cc_start: 0.6134 (mtt180) cc_final: 0.5915 (mtt180) REVERT: E 36 ASP cc_start: 0.8153 (m-30) cc_final: 0.7924 (m-30) REVERT: E 194 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8245 (ttm170) REVERT: F 6 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8288 (tp) REVERT: F 75 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9045 (pt) REVERT: F 79 MET cc_start: 0.8669 (mmm) cc_final: 0.8421 (mmm) REVERT: F 841 ASP cc_start: 0.7879 (t0) cc_final: 0.7647 (t0) REVERT: F 853 THR cc_start: 0.9247 (m) cc_final: 0.8601 (p) REVERT: F 871 GLU cc_start: 0.7802 (tt0) cc_final: 0.7518 (tt0) REVERT: G 53 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5506 (mt) REVERT: G 60 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7638 (pt0) REVERT: G 184 ASP cc_start: 0.7879 (t0) cc_final: 0.7613 (t70) REVERT: H 73 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6330 (pp) REVERT: H 158 ILE cc_start: 0.8942 (mp) cc_final: 0.8689 (tt) REVERT: H 178 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7185 (t70) REVERT: I 54 MET cc_start: 0.6483 (mmm) cc_final: 0.5791 (mmm) REVERT: J 135 ASP cc_start: 0.7642 (t0) cc_final: 0.7249 (t0) REVERT: J 145 ASN cc_start: 0.8676 (t0) cc_final: 0.8086 (t0) REVERT: J 182 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6378 (mt-10) REVERT: J 841 ASP cc_start: 0.7858 (t0) cc_final: 0.7650 (t0) REVERT: J 853 THR cc_start: 0.9248 (m) cc_final: 0.8760 (p) REVERT: J 871 GLU cc_start: 0.7794 (tt0) cc_final: 0.7543 (tt0) REVERT: K 178 ASP cc_start: 0.8231 (t0) cc_final: 0.7920 (t0) REVERT: K 195 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: L 54 ARG cc_start: 0.6558 (mtt180) cc_final: 0.6283 (mtt180) REVERT: L 158 ILE cc_start: 0.9177 (mm) cc_final: 0.8879 (tp) outliers start: 153 outliers final: 125 residues processed: 492 average time/residue: 0.1494 time to fit residues: 115.6194 Evaluate side-chains 484 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 352 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 875 ASP Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 195 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 801 THR Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 125 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 218 optimal weight: 0.0970 chunk 214 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 overall best weight: 2.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 HIS ** L 46 HIS ** 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 = 0.3238 r_free = 0.3238 target = 0.097348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.086411 restraints weight = 55267.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088812 restraints weight = 29314.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090377 restraints weight = 18138.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091471 restraints weight = 12423.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092262 restraints weight = 9135.009| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23100 Z= 0.195 Angle : 0.819 16.882 31347 Z= 0.394 Chirality : 0.049 0.360 3408 Planarity : 0.005 0.057 4188 Dihedral : 6.347 48.655 3300 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 6.31 % Allowed : 25.32 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.14), residues: 2943 helix: -1.15 (0.27), residues: 378 sheet: -1.97 (0.22), residues: 504 loop : -2.65 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 69 TYR 0.023 0.002 TYR I 73 PHE 0.044 0.002 PHE L 76 TRP 0.046 0.002 TRP F 87 HIS 0.011 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00438 (23088) covalent geometry : angle 0.76622 (31311) hydrogen bonds : bond 0.03151 ( 378) hydrogen bonds : angle 6.86913 ( 927) metal coordination : bond 0.01826 ( 12) metal coordination : angle 8.57158 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 378 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8621 (p90) cc_final: 0.8328 (p90) REVERT: C 65 LEU cc_start: 0.9267 (mm) cc_final: 0.9034 (mm) REVERT: C 279 MET cc_start: 0.9268 (tpt) cc_final: 0.8958 (tpt) REVERT: D 54 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: D 79 MET cc_start: 0.8663 (mmm) cc_final: 0.8426 (mmm) REVERT: D 841 ASP cc_start: 0.7864 (t0) cc_final: 0.7646 (t0) REVERT: D 853 THR cc_start: 0.9214 (m) cc_final: 0.8675 (p) REVERT: B 60 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7713 (pt0) REVERT: B 67 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 178 ASP cc_start: 0.8231 (t0) cc_final: 0.6860 (t0) REVERT: A 158 ILE cc_start: 0.9213 (mp) cc_final: 0.8958 (tp) REVERT: E 36 ASP cc_start: 0.8262 (m-30) cc_final: 0.8028 (m-30) REVERT: E 108 MET cc_start: 0.8470 (tpt) cc_final: 0.8247 (tpp) REVERT: E 194 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8328 (ttm170) REVERT: F 6 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8244 (tp) REVERT: F 75 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9001 (pt) REVERT: F 79 MET cc_start: 0.8657 (mmm) cc_final: 0.8415 (mmm) REVERT: F 841 ASP cc_start: 0.7927 (t0) cc_final: 0.7622 (t0) REVERT: F 853 THR cc_start: 0.9229 (m) cc_final: 0.8614 (p) REVERT: G 5 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5613 (tt0) REVERT: G 53 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5434 (mt) REVERT: H 73 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6379 (pp) REVERT: H 178 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7236 (t70) REVERT: I 54 MET cc_start: 0.6483 (mmm) cc_final: 0.5821 (mmm) REVERT: I 108 MET cc_start: 0.8294 (tpt) cc_final: 0.7653 (tpt) REVERT: I 196 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8039 (p90) REVERT: I 277 ASP cc_start: 0.8230 (t0) cc_final: 0.7870 (t0) REVERT: J 135 ASP cc_start: 0.7578 (t0) cc_final: 0.7240 (t0) REVERT: J 145 ASN cc_start: 0.8694 (t0) cc_final: 0.8116 (t0) REVERT: J 182 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6416 (mt-10) REVERT: J 220 ARG cc_start: 0.4887 (OUTLIER) cc_final: 0.4348 (tmt170) REVERT: J 841 ASP cc_start: 0.7882 (t0) cc_final: 0.7666 (t0) REVERT: J 853 THR cc_start: 0.9237 (m) cc_final: 0.8746 (p) REVERT: J 871 GLU cc_start: 0.7706 (tt0) cc_final: 0.7347 (tt0) REVERT: K 195 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.4963 (m-80) REVERT: L 34 GLU cc_start: 0.7884 (pt0) cc_final: 0.7507 (pt0) REVERT: L 54 ARG cc_start: 0.6423 (mtt180) cc_final: 0.6127 (mtt180) REVERT: L 73 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6245 (pp) REVERT: L 158 ILE cc_start: 0.9208 (mm) cc_final: 0.8960 (tp) outliers start: 140 outliers final: 116 residues processed: 476 average time/residue: 0.1470 time to fit residues: 109.8770 Evaluate side-chains 481 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 354 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 195 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 220 ARG Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 801 THR Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 272 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083891 restraints weight = 56449.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086139 restraints weight = 30298.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087653 restraints weight = 18986.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088688 restraints weight = 13058.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.089436 restraints weight = 9743.653| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23100 Z= 0.237 Angle : 0.881 19.352 31347 Z= 0.417 Chirality : 0.051 0.376 3408 Planarity : 0.006 0.058 4188 Dihedral : 6.596 47.467 3300 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 6.67 % Allowed : 25.05 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.14), residues: 2943 helix: -0.80 (0.29), residues: 339 sheet: -2.05 (0.21), residues: 522 loop : -2.66 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 69 TYR 0.022 0.002 TYR I 73 PHE 0.054 0.002 PHE L 76 TRP 0.054 0.003 TRP D 87 HIS 0.012 0.002 HIS L 46 Details of bonding type rmsd covalent geometry : bond 0.00533 (23088) covalent geometry : angle 0.80773 (31311) hydrogen bonds : bond 0.03334 ( 378) hydrogen bonds : angle 6.98880 ( 927) metal coordination : bond 0.02329 ( 12) metal coordination : angle 10.44407 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 373 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8710 (p90) cc_final: 0.8296 (p90) REVERT: C 65 LEU cc_start: 0.9310 (mm) cc_final: 0.9070 (mm) REVERT: C 279 MET cc_start: 0.9325 (tpt) cc_final: 0.8996 (tpt) REVERT: D 54 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 79 MET cc_start: 0.8686 (mmm) cc_final: 0.8429 (mmm) REVERT: D 189 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8325 (p90) REVERT: D 841 ASP cc_start: 0.8021 (t0) cc_final: 0.7810 (t0) REVERT: D 853 THR cc_start: 0.9283 (m) cc_final: 0.8840 (p) REVERT: B 178 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (t0) REVERT: A 158 ILE cc_start: 0.9351 (mp) cc_final: 0.9118 (tp) REVERT: E 36 ASP cc_start: 0.8243 (m-30) cc_final: 0.7967 (m-30) REVERT: E 194 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8174 (ttm170) REVERT: F 75 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9021 (pt) REVERT: F 145 ASN cc_start: 0.8796 (t0) cc_final: 0.8366 (t0) REVERT: F 841 ASP cc_start: 0.7922 (t0) cc_final: 0.7663 (t0) REVERT: F 853 THR cc_start: 0.9235 (m) cc_final: 0.8624 (p) REVERT: G 5 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: G 53 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5500 (mt) REVERT: H 178 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7172 (t70) REVERT: I 54 MET cc_start: 0.6504 (mmm) cc_final: 0.5828 (mmm) REVERT: I 277 ASP cc_start: 0.8306 (t0) cc_final: 0.7937 (t0) REVERT: J 135 ASP cc_start: 0.7695 (t0) cc_final: 0.7363 (t0) REVERT: J 145 ASN cc_start: 0.8737 (t0) cc_final: 0.8103 (t0) REVERT: J 220 ARG cc_start: 0.4935 (OUTLIER) cc_final: 0.4413 (tmt170) REVERT: J 841 ASP cc_start: 0.7837 (t0) cc_final: 0.7635 (t0) REVERT: J 853 THR cc_start: 0.9253 (m) cc_final: 0.8763 (p) REVERT: J 871 GLU cc_start: 0.7695 (tt0) cc_final: 0.7254 (tt0) REVERT: L 34 GLU cc_start: 0.7950 (pt0) cc_final: 0.7536 (pt0) REVERT: L 54 ARG cc_start: 0.6438 (mtt180) cc_final: 0.6156 (mtt180) REVERT: L 158 ILE cc_start: 0.9265 (mm) cc_final: 0.8905 (tp) outliers start: 148 outliers final: 123 residues processed: 478 average time/residue: 0.1452 time to fit residues: 110.0932 Evaluate side-chains 485 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 354 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 195 PHE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 220 ARG Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 801 THR Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 42 optimal weight: 0.0170 chunk 247 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 244 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** 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 = 0.3302 r_free = 0.3302 target = 0.101416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090605 restraints weight = 54588.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.093054 restraints weight = 28942.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094654 restraints weight = 17765.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095689 restraints weight = 12010.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096392 restraints weight = 8876.977| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23100 Z= 0.139 Angle : 0.809 16.717 31347 Z= 0.391 Chirality : 0.048 0.376 3408 Planarity : 0.005 0.057 4188 Dihedral : 5.962 43.452 3300 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.23 % Allowed : 27.97 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.14), residues: 2943 helix: -0.97 (0.27), residues: 366 sheet: -1.97 (0.22), residues: 522 loop : -2.55 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 77 TYR 0.023 0.001 TYR C 73 PHE 0.041 0.001 PHE L 76 TRP 0.053 0.002 TRP F 87 HIS 0.009 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00299 (23088) covalent geometry : angle 0.77553 (31311) hydrogen bonds : bond 0.02855 ( 378) hydrogen bonds : angle 6.85887 ( 927) metal coordination : bond 0.00957 ( 12) metal coordination : angle 6.82136 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 427 time to evaluate : 0.730 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: C 65 LEU cc_start: 0.9066 (mm) cc_final: 0.8836 (mm) REVERT: C 103 TRP cc_start: 0.8687 (p-90) cc_final: 0.7942 (p-90) REVERT: C 211 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7526 (tt) REVERT: D 54 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: D 79 MET cc_start: 0.8656 (mmm) cc_final: 0.8362 (mmm) REVERT: D 853 THR cc_start: 0.9176 (m) cc_final: 0.8796 (p) REVERT: B 60 GLU cc_start: 0.8027 (tt0) cc_final: 0.7824 (tt0) REVERT: B 178 ASP cc_start: 0.7972 (t0) cc_final: 0.6735 (t0) REVERT: A 54 ARG cc_start: 0.6230 (mtt180) cc_final: 0.6001 (mtt180) REVERT: A 158 ILE cc_start: 0.9410 (mp) cc_final: 0.9159 (tp) REVERT: E 194 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8571 (ttm170) REVERT: F 145 ASN cc_start: 0.8800 (t0) cc_final: 0.8454 (t0) REVERT: F 160 LYS cc_start: 0.8732 (pttm) cc_final: 0.8216 (tptp) REVERT: F 189 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: F 841 ASP cc_start: 0.7835 (t0) cc_final: 0.7595 (t0) REVERT: F 853 THR cc_start: 0.9178 (m) cc_final: 0.8698 (p) REVERT: F 897 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7513 (mm-30) REVERT: G 53 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5450 (mt) REVERT: G 56 LEU cc_start: 0.9043 (mm) cc_final: 0.8529 (pp) REVERT: H 178 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7167 (t70) REVERT: I 59 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8950 (t) REVERT: I 108 MET cc_start: 0.8308 (tpt) cc_final: 0.7644 (tpt) REVERT: I 277 ASP cc_start: 0.8078 (t0) cc_final: 0.7655 (t0) REVERT: J 145 ASN cc_start: 0.8807 (t0) cc_final: 0.8439 (t0) REVERT: J 220 ARG cc_start: 0.4917 (OUTLIER) cc_final: 0.4340 (tmt170) REVERT: J 841 ASP cc_start: 0.7835 (t0) cc_final: 0.7606 (t0) REVERT: J 853 THR cc_start: 0.9188 (m) cc_final: 0.8672 (p) REVERT: J 871 GLU cc_start: 0.7698 (tt0) cc_final: 0.7379 (tt0) REVERT: K 202 GLN cc_start: 0.7496 (mp10) cc_final: 0.7287 (mp10) REVERT: L 34 GLU cc_start: 0.7575 (pt0) cc_final: 0.7289 (pt0) REVERT: L 54 ARG cc_start: 0.6383 (mtt180) cc_final: 0.6052 (mtt180) outliers start: 94 outliers final: 68 residues processed: 489 average time/residue: 0.1510 time to fit residues: 114.7976 Evaluate side-chains 451 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 376 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 851 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 745 TRP Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 195 PHE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 220 ARG Chi-restraints excluded: chain J residue 745 TRP Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 83 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 231 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS I 140 GLN ** I 266 ASN ** 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 = 0.3268 r_free = 0.3268 target = 0.099206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.088469 restraints weight = 55082.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090840 restraints weight = 29332.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092356 restraints weight = 18161.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093450 restraints weight = 12508.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094207 restraints weight = 9205.775| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23100 Z= 0.166 Angle : 0.823 15.794 31347 Z= 0.394 Chirality : 0.049 0.390 3408 Planarity : 0.005 0.055 4188 Dihedral : 6.046 41.625 3300 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 4.14 % Allowed : 28.69 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.14), residues: 2943 helix: -0.85 (0.28), residues: 366 sheet: -1.88 (0.22), residues: 516 loop : -2.55 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 209 TYR 0.023 0.001 TYR I 73 PHE 0.052 0.002 PHE A 76 TRP 0.057 0.002 TRP D 87 HIS 0.013 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00370 (23088) covalent geometry : angle 0.77331 (31311) hydrogen bonds : bond 0.03011 ( 378) hydrogen bonds : angle 6.77699 ( 927) metal coordination : bond 0.01339 ( 12) metal coordination : angle 8.31740 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3206.02 seconds wall clock time: 56 minutes 5.44 seconds (3365.44 seconds total)