Starting phenix.real_space_refine on Wed Nov 19 08:13:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6teh_10490/11_2025/6teh_10490.cif Found real_map, /net/cci-nas-00/data/ceres_data/6teh_10490/11_2025/6teh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6teh_10490/11_2025/6teh_10490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6teh_10490/11_2025/6teh_10490.map" model { file = "/net/cci-nas-00/data/ceres_data/6teh_10490/11_2025/6teh_10490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6teh_10490/11_2025/6teh_10490.cif" } 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-2.0-5881/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: 4.68, per 1000 atoms: 0.21 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: 1.90 Conformation dependent library (CDL) restraints added in 823.6 milliseconds 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: 0.92 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: 3.48 Time building geometry restraints manager: 2.47 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: 0.05 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.030 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- 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 : 0.791 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: 0.7418 (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: 0.8440 (mm-40) REVERT: E 83 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8401 (tm-30) REVERT: E 99 TRP cc_start: 0.8829 (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: 0.7313 (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: 0.8743 (mm) REVERT: I 83 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8621 (tm-30) REVERT: J 135 ASP cc_start: 0.7402 (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: 0.7271 (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: 0.8373 (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: 0.1787 time to fit residues: 187.5399 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 : 1.031 ------------------------------------------------------------------------------- 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 : 0.864 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: 0.8093 (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: 0.7127 (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: 0.8928 (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: 0.6268 (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: 0.8415 (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: 0.1521 time to fit residues: 146.8334 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 : 0.923 ------------------------------------------------------------------------------- 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 : 0.834 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: 0.7480 (t0) REVERT: D 853 THR cc_start: 0.9275 (m) cc_final: 0.8714 (p) REVERT: D 871 GLU cc_start: 0.8066 (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: 0.7968 (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: 0.7989 (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: 0.8087 (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: 0.9023 (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: 0.8716 (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: 0.1594 time to fit residues: 133.8289 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 : 0.850 ------------------------------------------------------------------------------- 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 : 0.828 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: 0.8015 (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: 0.7239 (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: 0.8258 (m-30) cc_final: 0.7904 (m-30) REVERT: E 54 MET cc_start: 0.6179 (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: 0.7365 (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: 0.7764 (OUTLIER) cc_final: 0.7390 (t70) REVERT: J 135 ASP cc_start: 0.7483 (t0) cc_final: 0.7245 (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: 0.7808 (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: 0.1558 time to fit residues: 127.4320 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 : 0.871 ------------------------------------------------------------------------------- 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 : 0.704 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: 0.8309 (OUTLIER) cc_final: 0.7290 (p90) REVERT: F 75 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9059 (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: 0.7953 (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: 0.8129 (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: 0.7559 (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: 0.7766 (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: 0.8287 (OUTLIER) cc_final: 0.8085 (mp) REVERT: K 184 ASP cc_start: 0.7923 (t0) cc_final: 0.7608 (t70) 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: 0.1668 time to fit residues: 128.7815 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 : 0.765 ------------------------------------------------------------------------------- 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 = 0.098211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087235 restraints weight = 55444.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089638 restraints weight = 29496.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091191 restraints weight = 18217.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.092263 restraints weight = 12494.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093038 restraints weight = 9221.470| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4706 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 16.551 31347 Z= 0.379 Chirality : 0.048 0.317 3408 Planarity : 0.005 0.059 4188 Dihedral : 6.324 54.255 3300 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.69 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 0.001 ARG K 69 TYR 0.022 0.002 TYR I 73 PHE 0.037 0.002 PHE G 76 TRP 0.037 0.002 TRP J 87 HIS 0.009 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00407 (23088) covalent geometry : angle 0.73626 (31311) hydrogen bonds : bond 0.03256 ( 378) hydrogen bonds : angle 6.88565 ( 927) metal coordination : bond 0.01672 ( 12) metal coordination : angle 8.26498 ( 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 551 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 405 time to evaluate : 0.894 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: 0.8629 (p90) cc_final: 0.8292 (p90) REVERT: C 65 LEU cc_start: 0.9268 (mm) cc_final: 0.9010 (mm) REVERT: C 279 MET cc_start: 0.9260 (tpt) cc_final: 0.8950 (tpt) REVERT: D 54 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: D 841 ASP cc_start: 0.7785 (t0) cc_final: 0.7527 (t0) REVERT: D 853 THR cc_start: 0.9213 (m) cc_final: 0.8664 (p) REVERT: B 60 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7690 (pt0) REVERT: B 178 ASP cc_start: 0.8206 (t0) cc_final: 0.6892 (t0) REVERT: B 184 ASP cc_start: 0.7841 (t0) cc_final: 0.7623 (t70) REVERT: E 196 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7230 (p90) REVERT: F 6 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8135 (tp) REVERT: F 75 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8992 (pt) REVERT: F 841 ASP cc_start: 0.7885 (t0) cc_final: 0.7635 (t0) REVERT: F 853 THR cc_start: 0.9239 (m) cc_final: 0.8587 (p) REVERT: G 60 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7774 (pt0) REVERT: G 184 ASP cc_start: 0.7885 (t0) cc_final: 0.7617 (t70) REVERT: H 25 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: H 67 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6804 (tm-30) REVERT: H 158 ILE cc_start: 0.8883 (mp) cc_final: 0.8588 (tt) REVERT: H 178 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7222 (t70) REVERT: I 229 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7263 (mm-30) REVERT: J 135 ASP cc_start: 0.7625 (t0) cc_final: 0.7252 (t0) REVERT: J 145 ASN cc_start: 0.8659 (t0) cc_final: 0.8015 (t0) REVERT: J 182 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6394 (mt-10) REVERT: J 841 ASP cc_start: 0.7876 (t0) cc_final: 0.7642 (t0) REVERT: J 853 THR cc_start: 0.9266 (m) cc_final: 0.8767 (p) REVERT: J 871 GLU cc_start: 0.7777 (tt0) cc_final: 0.7274 (tt0) REVERT: K 60 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7810 (pt0) REVERT: K 158 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8181 (mp) REVERT: K 178 ASP cc_start: 0.8240 (t0) cc_final: 0.6936 (t0) REVERT: K 184 ASP cc_start: 0.7979 (t0) cc_final: 0.7644 (t0) REVERT: L 158 ILE cc_start: 0.8906 (mm) cc_final: 0.8544 (tp) outliers start: 146 outliers final: 117 residues processed: 511 average time/residue: 0.1558 time to fit residues: 125.7462 Evaluate side-chains 489 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 365 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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 72 GLN ** 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 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 = 0.3181 r_free = 0.3181 target = 0.093861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.083056 restraints weight = 56654.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085338 restraints weight = 30774.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.086792 restraints weight = 19420.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.087846 restraints weight = 13565.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088622 restraints weight = 10128.607| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 23100 Z= 0.278 Angle : 0.907 18.910 31347 Z= 0.426 Chirality : 0.051 0.338 3408 Planarity : 0.006 0.060 4188 Dihedral : 6.802 50.653 3300 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.85 % Favored : 85.15 % Rotamer: Outliers : 7.03 % Allowed : 23.78 % 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: -3.40 (0.14), residues: 2943 helix: -1.00 (0.29), residues: 339 sheet: -2.00 (0.23), residues: 459 loop : -2.75 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 69 TYR 0.021 0.002 TYR I 73 PHE 0.051 0.002 PHE L 76 TRP 0.041 0.003 TRP J 87 HIS 0.010 0.002 HIS L 46 Details of bonding type rmsd covalent geometry : bond 0.00625 (23088) covalent geometry : angle 0.82022 (31311) hydrogen bonds : bond 0.03671 ( 378) hydrogen bonds : angle 7.09372 ( 927) metal coordination : bond 0.02706 ( 12) metal coordination : angle 11.43439 ( 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 533 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 377 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8764 (p90) cc_final: 0.8366 (p90) REVERT: C 65 LEU cc_start: 0.9367 (mm) cc_final: 0.9093 (mm) REVERT: C 229 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 279 MET cc_start: 0.9300 (tpt) cc_final: 0.8971 (tpt) REVERT: D 54 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: D 79 MET cc_start: 0.8689 (mmm) cc_final: 0.8421 (mmm) REVERT: D 189 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8302 (p90) REVERT: D 853 THR cc_start: 0.9299 (m) cc_final: 0.8708 (p) REVERT: B 60 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7739 (pt0) REVERT: B 184 ASP cc_start: 0.7998 (t0) cc_final: 0.7778 (t70) REVERT: A 158 ILE cc_start: 0.9192 (mp) cc_final: 0.8935 (tp) REVERT: E 36 ASP cc_start: 0.8296 (m-30) cc_final: 0.8013 (m-30) REVERT: E 194 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8209 (ttm170) REVERT: F 75 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9059 (pt) REVERT: F 841 ASP cc_start: 0.7891 (t0) cc_final: 0.7607 (t0) REVERT: F 853 THR cc_start: 0.9284 (m) cc_final: 0.8582 (p) REVERT: F 897 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7683 (mp0) REVERT: G 5 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5897 (tt0) REVERT: G 53 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5486 (mt) REVERT: G 184 ASP cc_start: 0.7946 (t0) cc_final: 0.7656 (t70) REVERT: H 158 ILE cc_start: 0.8980 (mp) cc_final: 0.8752 (tt) REVERT: H 178 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7276 (t70) REVERT: I 54 MET cc_start: 0.6607 (mmm) cc_final: 0.5929 (mmm) REVERT: I 116 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8324 (m90) REVERT: I 196 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8105 (p90) REVERT: J 135 ASP cc_start: 0.7776 (t0) cc_final: 0.7475 (t0) REVERT: J 145 ASN cc_start: 0.8655 (t0) cc_final: 0.8022 (t0) REVERT: J 841 ASP cc_start: 0.7841 (t0) cc_final: 0.7636 (t0) REVERT: J 853 THR cc_start: 0.9301 (m) cc_final: 0.8806 (p) REVERT: J 871 GLU cc_start: 0.7801 (tt0) cc_final: 0.7569 (tt0) REVERT: K 67 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7086 (tm-30) REVERT: K 195 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.4990 (m-80) REVERT: L 54 ARG cc_start: 0.6541 (mtt180) cc_final: 0.6256 (mtt180) REVERT: L 158 ILE cc_start: 0.9220 (mm) cc_final: 0.8901 (tp) outliers start: 156 outliers final: 121 residues processed: 489 average time/residue: 0.1558 time to fit residues: 119.2873 Evaluate side-chains 470 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 340 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 54 MET 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 273 ILE 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 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 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 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 176 ILE Chi-restraints excluded: chain F residue 189 PHE 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 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 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 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 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 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 Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 125 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** B 72 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN 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 = 0.3283 r_free = 0.3283 target = 0.100135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089352 restraints weight = 54413.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091730 restraints weight = 29169.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093265 restraints weight = 18156.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094354 restraints weight = 12480.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095138 restraints weight = 9180.939| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23100 Z= 0.140 Angle : 0.795 14.576 31347 Z= 0.385 Chirality : 0.048 0.340 3408 Planarity : 0.005 0.060 4188 Dihedral : 6.159 47.066 3300 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 5.36 % Allowed : 26.67 % Favored : 67.97 % 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: -3.23 (0.14), residues: 2943 helix: -1.05 (0.28), residues: 360 sheet: -2.02 (0.23), residues: 441 loop : -2.56 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 69 TYR 0.027 0.001 TYR E 73 PHE 0.046 0.001 PHE L 76 TRP 0.048 0.002 TRP F 87 HIS 0.011 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00304 (23088) covalent geometry : angle 0.75750 (31311) hydrogen bonds : bond 0.02984 ( 378) hydrogen bonds : angle 6.87206 ( 927) metal coordination : bond 0.01069 ( 12) metal coordination : angle 7.19957 ( 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 524 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 405 time to evaluate : 0.796 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: C 65 LEU cc_start: 0.9172 (mm) cc_final: 0.8889 (mm) REVERT: C 211 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7552 (tt) REVERT: C 279 MET cc_start: 0.9194 (tpt) cc_final: 0.8889 (tpt) REVERT: D 54 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: D 183 ASP cc_start: 0.8208 (m-30) cc_final: 0.8007 (m-30) REVERT: D 841 ASP cc_start: 0.7830 (t0) cc_final: 0.7598 (t0) REVERT: D 853 THR cc_start: 0.9233 (m) cc_final: 0.8806 (p) REVERT: B 178 ASP cc_start: 0.8097 (t0) cc_final: 0.6681 (t0) REVERT: A 158 ILE cc_start: 0.9212 (mp) cc_final: 0.8969 (tp) REVERT: E 194 ARG cc_start: 0.8853 (ttm110) cc_final: 0.8230 (ttm170) REVERT: F 6 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8217 (tp) REVERT: F 145 ASN cc_start: 0.8772 (t0) cc_final: 0.8351 (t0) REVERT: F 189 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: F 841 ASP cc_start: 0.7854 (t0) cc_final: 0.7629 (t0) REVERT: F 853 THR cc_start: 0.9182 (m) cc_final: 0.8519 (p) REVERT: G 5 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5513 (tt0) REVERT: G 53 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5145 (mt) REVERT: G 56 LEU cc_start: 0.9067 (mm) cc_final: 0.8494 (pp) REVERT: G 182 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7222 (ppt-90) REVERT: G 184 ASP cc_start: 0.7884 (t0) cc_final: 0.7549 (t70) REVERT: H 58 ASP cc_start: 0.7319 (t0) cc_final: 0.7074 (t0) REVERT: H 178 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7247 (t70) REVERT: I 108 MET cc_start: 0.8299 (tpt) cc_final: 0.7690 (tpt) REVERT: I 277 ASP cc_start: 0.8169 (t0) cc_final: 0.7786 (t0) REVERT: J 145 ASN cc_start: 0.8750 (t0) cc_final: 0.8247 (t0) REVERT: J 220 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.4307 (tmt170) REVERT: J 841 ASP cc_start: 0.7813 (t0) cc_final: 0.7589 (t0) REVERT: J 853 THR cc_start: 0.9204 (m) cc_final: 0.8721 (p) REVERT: J 871 GLU cc_start: 0.7700 (tt0) cc_final: 0.7478 (tt0) REVERT: K 178 ASP cc_start: 0.8152 (t0) cc_final: 0.7827 (t0) REVERT: K 195 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.5096 (m-80) REVERT: L 34 GLU cc_start: 0.7632 (pt0) cc_final: 0.7267 (pt0) REVERT: L 54 ARG cc_start: 0.6383 (mtt180) cc_final: 0.6145 (mtt180) REVERT: L 158 ILE cc_start: 0.9225 (mm) cc_final: 0.9008 (tp) outliers start: 119 outliers final: 85 residues processed: 481 average time/residue: 0.1613 time to fit residues: 120.9935 Evaluate side-chains 473 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 378 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 35 THR 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 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 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 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 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 82 THR 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 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 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 G residue 5 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 73 LEU Chi-restraints excluded: chain G residue 182 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 H residue 56 LEU 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 204 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 86 ILE 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 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 J residue 938 THR Chi-restraints excluded: chain K residue 30 SER 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 K residue 195 PHE Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP 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: 7.9990 chunk 98 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 256 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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 ** 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 72 GLN ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.081502 restraints weight = 57254.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083782 restraints weight = 30026.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.085374 restraints weight = 18839.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.086419 restraints weight = 12885.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.087201 restraints weight = 9598.198| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 23100 Z= 0.317 Angle : 0.966 21.347 31347 Z= 0.451 Chirality : 0.053 0.339 3408 Planarity : 0.006 0.071 4188 Dihedral : 6.910 47.545 3300 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.98 % Favored : 85.02 % Rotamer: Outliers : 6.22 % Allowed : 26.13 % Favored : 67.66 % 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: -0.88 (0.29), residues: 339 sheet: -2.16 (0.21), residues: 528 loop : -2.74 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 69 TYR 0.021 0.002 TYR J 794 PHE 0.057 0.002 PHE L 76 TRP 0.058 0.003 TRP C 22 HIS 0.016 0.002 HIS L 46 Details of bonding type rmsd covalent geometry : bond 0.00712 (23088) covalent geometry : angle 0.86683 (31311) hydrogen bonds : bond 0.03687 ( 378) hydrogen bonds : angle 7.10890 ( 927) metal coordination : bond 0.02915 ( 12) metal coordination : angle 12.61659 ( 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 510 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 372 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 279 MET cc_start: 0.9354 (tpt) cc_final: 0.9000 (tpt) REVERT: D 54 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: D 79 MET cc_start: 0.8688 (mmm) cc_final: 0.8461 (mmm) REVERT: D 145 ASN cc_start: 0.8637 (t0) cc_final: 0.8082 (t0) REVERT: D 189 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8386 (p90) REVERT: D 853 THR cc_start: 0.9313 (m) cc_final: 0.8719 (p) REVERT: B 5 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5932 (tt0) REVERT: B 178 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.6812 (t0) REVERT: E 194 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8307 (ttm170) REVERT: F 75 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9000 (pt) REVERT: F 145 ASN cc_start: 0.8758 (t0) cc_final: 0.8293 (t0) REVERT: F 841 ASP cc_start: 0.7957 (t0) cc_final: 0.7722 (t0) REVERT: F 853 THR cc_start: 0.9295 (m) cc_final: 0.8598 (p) REVERT: G 5 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6066 (tt0) REVERT: G 53 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5385 (mt) REVERT: G 182 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7545 (ppt-90) REVERT: G 184 ASP cc_start: 0.8021 (t0) cc_final: 0.7566 (t0) REVERT: H 178 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7212 (t70) REVERT: I 116 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8284 (m90) REVERT: I 196 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8072 (p90) REVERT: J 145 ASN cc_start: 0.8772 (t0) cc_final: 0.8166 (t0) REVERT: J 853 THR cc_start: 0.9300 (m) cc_final: 0.8800 (p) REVERT: J 871 GLU cc_start: 0.7765 (tt0) cc_final: 0.7319 (tt0) REVERT: K 67 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7253 (tm-30) REVERT: L 34 GLU cc_start: 0.8115 (pt0) cc_final: 0.7655 (pt0) REVERT: L 54 ARG cc_start: 0.6543 (mtt180) cc_final: 0.6190 (mtt180) REVERT: L 158 ILE cc_start: 0.9281 (mm) cc_final: 0.8943 (tp) outliers start: 138 outliers final: 108 residues processed: 474 average time/residue: 0.1579 time to fit residues: 117.3563 Evaluate side-chains 470 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 351 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 130 GLU 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 290 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 40 VAL 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 902 LEU Chi-restraints excluded: chain D residue 920 VAL 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 5 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 178 ASP 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 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 76 LEU Chi-restraints excluded: chain E residue 82 THR 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 239 VAL 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 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 11 ASN 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 182 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 185 THR 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 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 196 PHE 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 189 PHE 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 J residue 938 THR 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 27 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: 0.9980 chunk 247 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 145 optimal weight: 0.0870 chunk 220 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 ** 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 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.087182 restraints weight = 55556.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.089389 restraints weight = 29835.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090963 restraints weight = 18834.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091962 restraints weight = 12787.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092712 restraints weight = 9487.679| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23100 Z= 0.168 Angle : 0.840 16.447 31347 Z= 0.405 Chirality : 0.049 0.413 3408 Planarity : 0.005 0.058 4188 Dihedral : 6.362 44.602 3300 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 5.05 % Allowed : 27.66 % Favored : 67.30 % 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: -3.27 (0.14), residues: 2943 helix: -0.96 (0.28), residues: 360 sheet: -1.99 (0.22), residues: 504 loop : -2.63 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 69 TYR 0.023 0.001 TYR E 73 PHE 0.045 0.002 PHE L 76 TRP 0.056 0.002 TRP F 87 HIS 0.009 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00376 (23088) covalent geometry : angle 0.79350 (31311) hydrogen bonds : bond 0.03119 ( 378) hydrogen bonds : angle 6.94425 ( 927) metal coordination : bond 0.01446 ( 12) metal coordination : angle 8.14133 ( 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 484 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 372 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 MET cc_start: 0.8194 (tpt) cc_final: 0.7462 (tpt) REVERT: C 211 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7679 (tt) REVERT: C 279 MET cc_start: 0.9260 (tpt) cc_final: 0.8919 (tpt) REVERT: D 54 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: D 79 MET cc_start: 0.8660 (mmm) cc_final: 0.8418 (mmm) REVERT: D 183 ASP cc_start: 0.8245 (m-30) cc_final: 0.8037 (m-30) REVERT: D 853 THR cc_start: 0.9287 (m) cc_final: 0.8842 (p) REVERT: B 5 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5491 (tt0) REVERT: B 77 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8044 (ptm160) REVERT: B 178 ASP cc_start: 0.8116 (t0) cc_final: 0.7020 (t0) REVERT: E 54 MET cc_start: 0.6467 (mmt) cc_final: 0.6245 (mmp) REVERT: E 194 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8242 (ttm170) REVERT: F 6 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8220 (tp) REVERT: F 75 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8914 (pt) REVERT: F 189 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: F 841 ASP cc_start: 0.7864 (t0) cc_final: 0.7593 (t0) REVERT: F 853 THR cc_start: 0.9194 (m) cc_final: 0.8555 (p) REVERT: F 959 GLU cc_start: 0.7926 (pm20) cc_final: 0.7334 (pt0) REVERT: G 5 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5804 (tt0) REVERT: G 53 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5358 (mt) REVERT: G 61 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.7536 (ptp-170) REVERT: G 184 ASP cc_start: 0.7875 (t0) cc_final: 0.7672 (t70) REVERT: H 73 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6412 (pp) REVERT: H 178 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7220 (t70) REVERT: I 108 MET cc_start: 0.8358 (tpt) cc_final: 0.7616 (tpt) REVERT: I 277 ASP cc_start: 0.8206 (t0) cc_final: 0.7809 (t0) REVERT: J 145 ASN cc_start: 0.8759 (t0) cc_final: 0.8208 (t0) REVERT: J 182 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6404 (mt-10) REVERT: J 853 THR cc_start: 0.9218 (m) cc_final: 0.8745 (p) REVERT: J 871 GLU cc_start: 0.7651 (tt0) cc_final: 0.7059 (tt0) REVERT: K 67 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7223 (tm-30) REVERT: L 34 GLU cc_start: 0.7849 (pt0) cc_final: 0.7410 (pt0) REVERT: L 54 ARG cc_start: 0.6371 (mtt180) cc_final: 0.6057 (mtt180) REVERT: L 73 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6372 (pp) REVERT: L 158 ILE cc_start: 0.9260 (mm) cc_final: 0.9024 (tp) outliers start: 112 outliers final: 81 residues processed: 457 average time/residue: 0.1651 time to fit residues: 117.4956 Evaluate side-chains 448 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 355 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 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 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 5 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 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 76 LEU Chi-restraints excluded: chain E residue 82 THR 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 E residue 290 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN 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 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 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 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 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 86 ILE Chi-restraints excluded: chain J residue 156 LEU 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 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR 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 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 200 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: 0.2980 chunk 245 optimal weight: 0.4980 chunk 160 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** 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 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089208 restraints weight = 54906.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.091577 restraints weight = 29213.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093088 restraints weight = 18013.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094158 restraints weight = 12346.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094924 restraints weight = 9090.175| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23100 Z= 0.147 Angle : 0.810 16.000 31347 Z= 0.390 Chirality : 0.048 0.361 3408 Planarity : 0.005 0.057 4188 Dihedral : 6.033 42.603 3300 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 4.68 % Allowed : 28.24 % Favored : 67.07 % 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: -3.16 (0.14), residues: 2943 helix: -0.86 (0.28), residues: 366 sheet: -1.93 (0.22), residues: 504 loop : -2.56 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 820 TYR 0.024 0.002 TYR E 73 PHE 0.047 0.002 PHE A 76 TRP 0.055 0.002 TRP F 87 HIS 0.010 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00324 (23088) covalent geometry : angle 0.76764 (31311) hydrogen bonds : bond 0.02927 ( 378) hydrogen bonds : angle 6.84072 ( 927) metal coordination : bond 0.01126 ( 12) metal coordination : angle 7.68287 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.56 seconds wall clock time: 59 minutes 47.57 seconds (3587.57 seconds total)