Starting phenix.real_space_refine on Wed Sep 17 20:16:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk8_19264/09_2025/8rk8_19264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk8_19264/09_2025/8rk8_19264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk8_19264/09_2025/8rk8_19264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk8_19264/09_2025/8rk8_19264.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk8_19264/09_2025/8rk8_19264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk8_19264/09_2025/8rk8_19264.cif" } resolution = 3.88 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 7194 2.51 5 N 1854 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11226 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1871 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 235} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.77, per 1000 atoms: 0.16 Number of scatterers: 11226 At special positions: 0 Unit cell: (150.882, 162.552, 59.1856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 2160 8.00 N 1854 7.00 C 7194 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 447.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 30 sheets defined 6.3% alpha, 54.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 142 through 145 Processing sheet with id=1, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.544A pdb=" N VAL A 19 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 184 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A 207 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 231 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA A 66 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A 42 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 64 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 40 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 66 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN A 38 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 68 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER A 36 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 70 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 34 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 72 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 32 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.406A pdb=" N THR A 184 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A 207 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=4, first strand: chain 'A' and resid 94 through 100 removed outlier: 5.249A pdb=" N SER A 95 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR A 169 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR A 97 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A 167 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU A 168 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU A 120 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.876A pdb=" N GLU A 148 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.544A pdb=" N VAL B 19 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 184 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 185 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS B 207 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 231 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 66 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU B 42 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS B 64 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA B 40 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA B 66 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 38 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 68 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER B 36 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 70 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 34 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 72 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 32 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 27 through 28 removed outlier: 4.406A pdb=" N THR B 184 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 185 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS B 207 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=9, first strand: chain 'B' and resid 94 through 100 removed outlier: 5.249A pdb=" N SER B 95 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR B 169 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR B 97 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 167 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU B 168 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU B 120 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 110 through 112 removed outlier: 4.876A pdb=" N GLU B 148 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.544A pdb=" N VAL C 19 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR C 184 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 185 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS C 207 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 231 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA C 66 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU C 42 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS C 64 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA C 40 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA C 66 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN C 38 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 68 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER C 36 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE C 70 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 34 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 72 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 32 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 27 through 28 removed outlier: 4.406A pdb=" N THR C 184 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 185 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS C 207 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 88 through 91 Processing sheet with id=14, first strand: chain 'C' and resid 94 through 100 removed outlier: 5.250A pdb=" N SER C 95 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR C 169 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR C 97 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C 167 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 168 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU C 120 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.876A pdb=" N GLU C 148 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.544A pdb=" N VAL D 19 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR D 184 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 185 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS D 207 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER D 231 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA D 66 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU D 42 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS D 64 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA D 40 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA D 66 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN D 38 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL D 68 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER D 36 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE D 70 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA D 34 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU D 72 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL D 32 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 27 through 28 removed outlier: 4.406A pdb=" N THR D 184 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 185 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS D 207 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=19, first strand: chain 'D' and resid 94 through 100 removed outlier: 5.249A pdb=" N SER D 95 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR D 169 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR D 97 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR D 167 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU D 168 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU D 120 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 110 through 112 removed outlier: 4.876A pdb=" N GLU D 148 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.544A pdb=" N VAL E 19 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR E 184 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS E 207 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER E 231 " --> pdb=" O ASP E 211 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 66 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU E 42 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS E 64 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA E 40 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA E 66 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN E 38 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL E 68 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER E 36 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE E 70 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 34 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU E 72 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL E 32 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.406A pdb=" N THR E 184 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS E 207 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 88 through 91 Processing sheet with id=24, first strand: chain 'E' and resid 94 through 100 removed outlier: 5.249A pdb=" N SER E 95 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR E 169 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR E 97 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR E 167 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU E 168 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU E 120 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 110 through 112 removed outlier: 4.876A pdb=" N GLU E 148 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.544A pdb=" N VAL F 19 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR F 184 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 185 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS F 207 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER F 231 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA F 66 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU F 42 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS F 64 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA F 40 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA F 66 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN F 38 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL F 68 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER F 36 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE F 70 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 34 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU F 72 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 32 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'F' and resid 27 through 28 removed outlier: 4.406A pdb=" N THR F 184 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 185 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS F 207 " --> pdb=" O VAL F 185 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 88 through 91 Processing sheet with id=29, first strand: chain 'F' and resid 94 through 100 removed outlier: 5.249A pdb=" N SER F 95 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR F 169 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR F 97 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR F 167 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU F 168 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU F 120 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 110 through 112 removed outlier: 4.876A pdb=" N GLU F 148 " --> pdb=" O ARG F 141 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1260 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: 1.66 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3672 1.34 - 1.46: 2134 1.46 - 1.57: 5606 1.57 - 1.69: 6 1.69 - 1.80: 36 Bond restraints: 11454 Sorted by residual: bond pdb=" C THR C 210 " pdb=" N ASP C 211 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.36e-02 5.41e+03 3.98e+00 bond pdb=" C THR B 210 " pdb=" N ASP B 211 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.36e-02 5.41e+03 3.96e+00 bond pdb=" C THR A 210 " pdb=" N ASP A 211 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.36e-02 5.41e+03 3.93e+00 bond pdb=" C THR D 210 " pdb=" N ASP D 211 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.36e-02 5.41e+03 3.93e+00 bond pdb=" C THR F 210 " pdb=" N ASP F 211 " ideal model delta sigma weight residual 1.331 1.357 -0.027 1.36e-02 5.41e+03 3.81e+00 ... (remaining 11449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 15332 1.61 - 3.21: 229 3.21 - 4.82: 63 4.82 - 6.42: 0 6.42 - 8.03: 6 Bond angle restraints: 15630 Sorted by residual: angle pdb=" CA PRO C 212 " pdb=" N PRO C 212 " pdb=" CD PRO C 212 " ideal model delta sigma weight residual 112.00 103.97 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" CA PRO B 212 " pdb=" N PRO B 212 " pdb=" CD PRO B 212 " ideal model delta sigma weight residual 112.00 103.99 8.01 1.40e+00 5.10e-01 3.27e+01 angle pdb=" CA PRO E 212 " pdb=" N PRO E 212 " pdb=" CD PRO E 212 " ideal model delta sigma weight residual 112.00 103.99 8.01 1.40e+00 5.10e-01 3.27e+01 angle pdb=" CA PRO D 212 " pdb=" N PRO D 212 " pdb=" CD PRO D 212 " ideal model delta sigma weight residual 112.00 104.00 8.00 1.40e+00 5.10e-01 3.26e+01 angle pdb=" CA PRO A 212 " pdb=" N PRO A 212 " pdb=" CD PRO A 212 " ideal model delta sigma weight residual 112.00 104.00 8.00 1.40e+00 5.10e-01 3.26e+01 ... (remaining 15625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6157 17.95 - 35.90: 521 35.90 - 53.86: 114 53.86 - 71.81: 24 71.81 - 89.76: 12 Dihedral angle restraints: 6828 sinusoidal: 2556 harmonic: 4272 Sorted by residual: dihedral pdb=" CB GLU C 48 " pdb=" CG GLU C 48 " pdb=" CD GLU C 48 " pdb=" OE1 GLU C 48 " ideal model delta sinusoidal sigma weight residual 0.00 89.76 -89.76 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 48 " pdb=" CG GLU B 48 " pdb=" CD GLU B 48 " pdb=" OE1 GLU B 48 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU E 48 " pdb=" CG GLU E 48 " pdb=" CD GLU E 48 " pdb=" OE1 GLU E 48 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 950 0.026 - 0.052: 529 0.052 - 0.078: 123 0.078 - 0.104: 99 0.104 - 0.131: 129 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA ILE F 192 " pdb=" N ILE F 192 " pdb=" C ILE F 192 " pdb=" CB ILE F 192 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 252 " pdb=" N ILE C 252 " pdb=" C ILE C 252 " pdb=" CB ILE C 252 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1827 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 211 " -0.082 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO C 212 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 211 " 0.082 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO E 212 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO E 212 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 212 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 211 " 0.082 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 212 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.063 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 102 1.40 - 2.28: 210 2.28 - 3.15: 9210 3.15 - 4.03: 26374 4.03 - 4.90: 49316 Warning: very small nonbonded interaction distances. Nonbonded interactions: 85212 Sorted by model distance: nonbonded pdb=" SD MET C 177 " pdb=" O GLY D 250 " model vdw 0.528 3.400 nonbonded pdb=" SD MET B 177 " pdb=" O GLY C 250 " model vdw 0.528 3.400 nonbonded pdb=" O GLY A 250 " pdb=" SD MET F 177 " model vdw 0.528 3.400 nonbonded pdb=" SD MET E 177 " pdb=" O GLY F 250 " model vdw 0.529 3.400 nonbonded pdb=" SD MET D 177 " pdb=" O GLY E 250 " model vdw 0.529 3.400 ... (remaining 85207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.037 0.954 11472 Z= 3.737 Angle : 0.550 8.027 15630 Z= 0.305 Chirality : 0.047 0.131 1830 Planarity : 0.008 0.119 2028 Dihedral : 14.928 89.759 4128 Min Nonbonded Distance : 0.528 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1500 helix: 0.59 (0.79), residues: 54 sheet: 0.62 (0.19), residues: 732 loop : -0.09 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 188 TYR 0.011 0.001 TYR E 169 PHE 0.007 0.001 PHE F 60 TRP 0.004 0.001 TRP C 28 HIS 0.001 0.000 HIS E 46 Details of bonding type rmsd covalent geometry : bond 0.00305 (11454) covalent geometry : angle 0.54999 (15630) hydrogen bonds : bond 0.15445 ( 360) hydrogen bonds : angle 6.19143 ( 1260) Misc. bond : bond 0.94293 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7092 (tpp80) REVERT: B 99 GLU cc_start: 0.6845 (tt0) cc_final: 0.6427 (tm-30) REVERT: C 182 GLN cc_start: 0.7457 (tt0) cc_final: 0.7014 (tt0) REVERT: D 47 LYS cc_start: 0.7645 (mttm) cc_final: 0.7311 (pptt) REVERT: D 71 THR cc_start: 0.8201 (m) cc_final: 0.7772 (m) REVERT: D 163 PHE cc_start: 0.7261 (m-10) cc_final: 0.6895 (m-10) REVERT: D 219 ILE cc_start: 0.7973 (mt) cc_final: 0.7692 (mt) REVERT: E 220 SER cc_start: 0.8253 (m) cc_final: 0.8046 (t) REVERT: E 223 ASN cc_start: 0.5435 (p0) cc_final: 0.4654 (t0) REVERT: F 223 ASN cc_start: 0.5367 (p0) cc_final: 0.4371 (t0) outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 0.1159 time to fit residues: 87.4148 Evaluate side-chains 324 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 79 ASN A 174 GLN A 223 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 38 GLN C 79 ASN C 136 GLN C 182 GLN D 20 ASN D 79 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 79 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090702 restraints weight = 37735.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092581 restraints weight = 22617.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093888 restraints weight = 15705.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094958 restraints weight = 11958.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095681 restraints weight = 9604.730| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.742 11472 Z= 1.624 Angle : 1.102 26.716 15630 Z= 0.540 Chirality : 0.054 0.236 1830 Planarity : 0.008 0.085 2028 Dihedral : 5.248 19.998 1620 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.90 % Allowed : 15.64 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1500 helix: 0.26 (0.68), residues: 54 sheet: 0.32 (0.20), residues: 720 loop : -0.04 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 27 TYR 0.026 0.003 TYR D 50 PHE 0.029 0.002 PHE D 60 TRP 0.019 0.004 TRP F 26 HIS 0.008 0.002 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.04689 (11454) covalent geometry : angle 1.10194 (15630) hydrogen bonds : bond 0.04336 ( 360) hydrogen bonds : angle 5.57077 ( 1260) Misc. bond : bond 0.00364 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 369 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8987 (t0) cc_final: 0.8634 (t0) REVERT: B 58 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.8113 (ttt-90) REVERT: B 99 GLU cc_start: 0.8018 (tt0) cc_final: 0.7415 (tm-30) REVERT: B 211 ASP cc_start: 0.8908 (t0) cc_final: 0.8413 (t0) REVERT: C 58 ARG cc_start: 0.8938 (tpt90) cc_final: 0.8702 (tpt90) REVERT: C 69 ASN cc_start: 0.8664 (m-40) cc_final: 0.8402 (m-40) REVERT: C 91 LYS cc_start: 0.8650 (tptt) cc_final: 0.8278 (tptm) REVERT: C 99 GLU cc_start: 0.7262 (tt0) cc_final: 0.6873 (tm-30) REVERT: C 163 PHE cc_start: 0.7631 (m-80) cc_final: 0.7278 (m-80) REVERT: D 6 TYR cc_start: 0.7853 (m-80) cc_final: 0.7624 (m-80) REVERT: D 47 LYS cc_start: 0.8909 (mttm) cc_final: 0.7569 (pptt) REVERT: D 53 GLN cc_start: 0.8666 (mt0) cc_final: 0.8464 (tt0) REVERT: D 99 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7568 (tm-30) REVERT: E 33 SER cc_start: 0.9290 (t) cc_final: 0.8807 (p) REVERT: E 223 ASN cc_start: 0.6808 (p0) cc_final: 0.6266 (t0) REVERT: F 148 GLU cc_start: 0.5944 (pm20) cc_final: 0.5519 (pm20) REVERT: F 223 ASN cc_start: 0.6905 (p0) cc_final: 0.6002 (t0) outliers start: 69 outliers final: 36 residues processed: 397 average time/residue: 0.1186 time to fit residues: 63.9107 Evaluate side-chains 333 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 230 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 125 optimal weight: 0.0570 chunk 68 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN D 223 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN E 182 GLN F 46 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089939 restraints weight = 38515.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091756 restraints weight = 22412.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093285 restraints weight = 15242.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094083 restraints weight = 11381.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094929 restraints weight = 9296.686| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.722 11472 Z= 1.614 Angle : 1.021 27.215 15630 Z= 0.490 Chirality : 0.052 0.307 1830 Planarity : 0.007 0.132 2028 Dihedral : 4.994 20.025 1620 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.81 % Allowed : 18.89 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1500 helix: -0.32 (0.67), residues: 54 sheet: 0.60 (0.20), residues: 714 loop : -0.01 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 112 TYR 0.020 0.002 TYR C 206 PHE 0.017 0.002 PHE D 60 TRP 0.018 0.002 TRP B 26 HIS 0.010 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.04661 (11454) covalent geometry : angle 1.02060 (15630) hydrogen bonds : bond 0.03916 ( 360) hydrogen bonds : angle 5.06320 ( 1260) Misc. bond : bond 0.00520 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 340 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7744 (tmt-80) REVERT: A 204 GLU cc_start: 0.7046 (tp30) cc_final: 0.6732 (mm-30) REVERT: A 246 LEU cc_start: 0.8435 (pt) cc_final: 0.8227 (pt) REVERT: B 43 LYS cc_start: 0.8266 (pttm) cc_final: 0.8029 (ptmt) REVERT: B 58 ARG cc_start: 0.8365 (ttt-90) cc_final: 0.8093 (tpt90) REVERT: B 99 GLU cc_start: 0.8000 (tt0) cc_final: 0.7503 (tm-30) REVERT: B 211 ASP cc_start: 0.8838 (t0) cc_final: 0.8621 (t0) REVERT: C 69 ASN cc_start: 0.8773 (m-40) cc_final: 0.8542 (m-40) REVERT: C 91 LYS cc_start: 0.8681 (tptt) cc_final: 0.8323 (tptm) REVERT: C 99 GLU cc_start: 0.7309 (tt0) cc_final: 0.6992 (tm-30) REVERT: C 112 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5330 (mtt180) REVERT: C 206 TYR cc_start: 0.8851 (m-80) cc_final: 0.8645 (m-80) REVERT: D 47 LYS cc_start: 0.8971 (mttm) cc_final: 0.7820 (pptt) REVERT: D 53 GLN cc_start: 0.8773 (mt0) cc_final: 0.8522 (tt0) REVERT: E 112 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7321 (mtt180) REVERT: E 141 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7867 (mtm110) REVERT: E 223 ASN cc_start: 0.7276 (p0) cc_final: 0.6737 (t0) REVERT: F 223 ASN cc_start: 0.7202 (p0) cc_final: 0.6254 (t0) REVERT: F 253 ILE cc_start: 0.8979 (mp) cc_final: 0.8693 (mm) REVERT: F 255 LEU cc_start: 0.9089 (tp) cc_final: 0.8561 (mm) outliers start: 68 outliers final: 41 residues processed: 371 average time/residue: 0.1313 time to fit residues: 64.7186 Evaluate side-chains 332 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 136 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 254 GLN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.083811 restraints weight = 39162.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085688 restraints weight = 22427.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086788 restraints weight = 15244.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088046 restraints weight = 11918.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088518 restraints weight = 9482.716| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.7609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.720 11472 Z= 1.485 Angle : 1.051 28.559 15630 Z= 0.511 Chirality : 0.052 0.277 1830 Planarity : 0.007 0.103 2028 Dihedral : 5.651 34.923 1620 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 7.18 % Allowed : 21.11 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1500 helix: 0.05 (0.68), residues: 54 sheet: 0.66 (0.20), residues: 672 loop : -0.14 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 112 TYR 0.047 0.002 TYR D 146 PHE 0.017 0.002 PHE D 60 TRP 0.032 0.003 TRP D 26 HIS 0.024 0.003 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.04274 (11454) covalent geometry : angle 1.05132 (15630) hydrogen bonds : bond 0.04433 ( 360) hydrogen bonds : angle 5.20272 ( 1260) Misc. bond : bond 0.00442 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8402 (ttt-90) cc_final: 0.7951 (ttp80) REVERT: A 99 GLU cc_start: 0.8655 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 204 GLU cc_start: 0.7685 (tp30) cc_final: 0.7420 (mm-30) REVERT: A 206 TYR cc_start: 0.8223 (m-80) cc_final: 0.8017 (m-80) REVERT: B 43 LYS cc_start: 0.8386 (pttm) cc_final: 0.8181 (ptmt) REVERT: B 85 TYR cc_start: 0.8288 (m-80) cc_final: 0.8017 (m-80) REVERT: B 99 GLU cc_start: 0.8399 (tt0) cc_final: 0.7693 (tm-30) REVERT: B 211 ASP cc_start: 0.8921 (t0) cc_final: 0.8698 (t0) REVERT: B 223 ASN cc_start: 0.7536 (p0) cc_final: 0.7294 (t0) REVERT: B 228 MET cc_start: 0.8299 (mtt) cc_final: 0.7948 (mtt) REVERT: C 99 GLU cc_start: 0.7728 (tt0) cc_final: 0.7498 (tm-30) REVERT: C 206 TYR cc_start: 0.8869 (m-80) cc_final: 0.8505 (m-80) REVERT: D 47 LYS cc_start: 0.9109 (mttm) cc_final: 0.7740 (pptt) REVERT: D 53 GLN cc_start: 0.8758 (mt0) cc_final: 0.8363 (tt0) REVERT: D 148 GLU cc_start: 0.5491 (mt-10) cc_final: 0.4924 (mt-10) REVERT: E 27 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7080 (ptm-80) REVERT: E 112 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6981 (ptp-110) REVERT: E 223 ASN cc_start: 0.7767 (p0) cc_final: 0.7029 (t0) REVERT: F 42 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: F 43 LYS cc_start: 0.8416 (pttm) cc_final: 0.8187 (pttm) REVERT: F 223 ASN cc_start: 0.7625 (p0) cc_final: 0.6727 (t0) outliers start: 84 outliers final: 55 residues processed: 340 average time/residue: 0.1382 time to fit residues: 62.1718 Evaluate side-chains 323 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 38 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 254 GLN D 46 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN F 46 HIS F 79 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.099217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087139 restraints weight = 37866.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089035 restraints weight = 21618.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090489 restraints weight = 14681.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091591 restraints weight = 10964.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092378 restraints weight = 8675.256| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.717 11472 Z= 1.474 Angle : 1.031 28.398 15630 Z= 0.493 Chirality : 0.051 0.283 1830 Planarity : 0.007 0.136 2028 Dihedral : 5.261 44.873 1620 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.96 % Allowed : 23.93 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: 0.31 (0.21), residues: 1500 helix: 0.30 (0.68), residues: 54 sheet: 0.62 (0.20), residues: 648 loop : -0.07 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 251 TYR 0.019 0.002 TYR B 146 PHE 0.020 0.001 PHE C 60 TRP 0.014 0.001 TRP D 26 HIS 0.017 0.002 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.04255 (11454) covalent geometry : angle 1.03069 (15630) hydrogen bonds : bond 0.03816 ( 360) hydrogen bonds : angle 4.95737 ( 1260) Misc. bond : bond 0.00667 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8534 (tt0) cc_final: 0.8325 (tm-30) REVERT: A 148 GLU cc_start: 0.7135 (pm20) cc_final: 0.6761 (pm20) REVERT: A 173 LYS cc_start: 0.8544 (pptt) cc_final: 0.8215 (pttp) REVERT: B 43 LYS cc_start: 0.8320 (pttm) cc_final: 0.8113 (ptmt) REVERT: B 85 TYR cc_start: 0.8313 (m-80) cc_final: 0.8100 (m-80) REVERT: B 99 GLU cc_start: 0.8194 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 223 ASN cc_start: 0.7421 (p0) cc_final: 0.7219 (t0) REVERT: C 58 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8380 (tpt90) REVERT: D 48 GLU cc_start: 0.6677 (pp20) cc_final: 0.6311 (tp30) REVERT: D 53 GLN cc_start: 0.8804 (mt0) cc_final: 0.8385 (tt0) REVERT: E 72 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8103 (pp) REVERT: E 112 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6883 (ptp-110) REVERT: E 148 GLU cc_start: 0.6951 (pm20) cc_final: 0.6141 (pm20) REVERT: E 223 ASN cc_start: 0.7784 (p0) cc_final: 0.7104 (t0) REVERT: F 48 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7749 (mm-30) REVERT: F 84 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8828 (mp) REVERT: F 91 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7780 (mtmt) REVERT: F 223 ASN cc_start: 0.7615 (p0) cc_final: 0.6660 (t0) REVERT: F 224 THR cc_start: 0.8996 (m) cc_final: 0.8566 (t) outliers start: 58 outliers final: 42 residues processed: 337 average time/residue: 0.1395 time to fit residues: 61.4443 Evaluate side-chains 310 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 245 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 39 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 79 ASN B 254 GLN C 38 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 254 GLN D 46 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN F 79 ASN F 136 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.078528 restraints weight = 39347.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080232 restraints weight = 22692.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.081513 restraints weight = 15556.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082398 restraints weight = 11746.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083105 restraints weight = 9569.578| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.8955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.722 11472 Z= 1.493 Angle : 1.094 28.514 15630 Z= 0.535 Chirality : 0.053 0.306 1830 Planarity : 0.008 0.208 2028 Dihedral : 6.006 45.334 1620 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 7.18 % Allowed : 23.85 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -0.08 (0.21), residues: 1500 helix: -0.06 (0.69), residues: 54 sheet: 0.51 (0.20), residues: 672 loop : -0.51 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 141 TYR 0.018 0.002 TYR B 146 PHE 0.014 0.002 PHE F 163 TRP 0.012 0.002 TRP C 26 HIS 0.030 0.004 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.04287 (11454) covalent geometry : angle 1.09374 (15630) hydrogen bonds : bond 0.04832 ( 360) hydrogen bonds : angle 5.21924 ( 1260) Misc. bond : bond 0.00701 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 261 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8492 (ttt-90) cc_final: 0.8045 (ttp80) REVERT: A 99 GLU cc_start: 0.8697 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 141 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7535 (ttm-80) REVERT: A 148 GLU cc_start: 0.7248 (pm20) cc_final: 0.6788 (pm20) REVERT: B 43 LYS cc_start: 0.8451 (pttm) cc_final: 0.8176 (ptmt) REVERT: B 53 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7630 (tp40) REVERT: B 85 TYR cc_start: 0.8581 (m-80) cc_final: 0.8250 (m-80) REVERT: B 99 GLU cc_start: 0.8504 (tt0) cc_final: 0.7954 (tm-30) REVERT: B 223 ASN cc_start: 0.7766 (p0) cc_final: 0.7157 (t0) REVERT: C 46 HIS cc_start: 0.7903 (t70) cc_final: 0.7574 (t70) REVERT: C 58 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8373 (tpt90) REVERT: C 211 ASP cc_start: 0.8912 (t70) cc_final: 0.8279 (t0) REVERT: C 223 ASN cc_start: 0.4741 (t0) cc_final: 0.4526 (t0) REVERT: D 53 GLN cc_start: 0.8747 (mt0) cc_final: 0.8216 (tt0) REVERT: D 115 ASN cc_start: 0.8518 (m110) cc_final: 0.8217 (m110) REVERT: E 72 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8328 (pp) REVERT: E 112 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7149 (ptp-110) REVERT: E 115 ASN cc_start: 0.8545 (m110) cc_final: 0.8279 (m-40) REVERT: E 148 GLU cc_start: 0.6869 (pm20) cc_final: 0.6265 (pm20) REVERT: F 48 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7797 (mm-30) REVERT: F 223 ASN cc_start: 0.7837 (p0) cc_final: 0.6705 (t0) REVERT: F 224 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8752 (t) outliers start: 84 outliers final: 63 residues processed: 308 average time/residue: 0.1356 time to fit residues: 55.6508 Evaluate side-chains 300 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 46 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN F 46 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079266 restraints weight = 38838.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081004 restraints weight = 22228.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082274 restraints weight = 15088.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083232 restraints weight = 11317.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083965 restraints weight = 9113.367| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.9271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.719 11472 Z= 1.480 Angle : 1.084 31.440 15630 Z= 0.515 Chirality : 0.051 0.311 1830 Planarity : 0.007 0.181 2028 Dihedral : 5.761 40.355 1620 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.64 % Allowed : 26.32 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -0.05 (0.21), residues: 1500 helix: 0.28 (0.67), residues: 54 sheet: 0.53 (0.20), residues: 672 loop : -0.52 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 141 TYR 0.021 0.002 TYR B 50 PHE 0.014 0.002 PHE F 163 TRP 0.010 0.001 TRP D 26 HIS 0.024 0.002 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.04265 (11454) covalent geometry : angle 1.08366 (15630) hydrogen bonds : bond 0.04315 ( 360) hydrogen bonds : angle 4.99945 ( 1260) Misc. bond : bond 0.00637 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8410 (tptp) REVERT: A 58 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.7957 (ttp80) REVERT: A 141 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7605 (ttm-80) REVERT: A 148 GLU cc_start: 0.7282 (pm20) cc_final: 0.6781 (pm20) REVERT: B 43 LYS cc_start: 0.8424 (pttm) cc_final: 0.8119 (ptpt) REVERT: B 53 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7941 (tp-100) REVERT: B 85 TYR cc_start: 0.8524 (m-80) cc_final: 0.8222 (m-80) REVERT: B 99 GLU cc_start: 0.8470 (tt0) cc_final: 0.7982 (tm-30) REVERT: B 100 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 223 ASN cc_start: 0.7856 (p0) cc_final: 0.7135 (t0) REVERT: C 43 LYS cc_start: 0.8735 (pttm) cc_final: 0.8295 (ptpt) REVERT: C 46 HIS cc_start: 0.7853 (t70) cc_final: 0.7542 (t70) REVERT: C 58 ARG cc_start: 0.8623 (tpt90) cc_final: 0.8363 (tpt90) REVERT: C 85 TYR cc_start: 0.8833 (m-80) cc_final: 0.8425 (m-80) REVERT: C 211 ASP cc_start: 0.8908 (t70) cc_final: 0.8456 (t0) REVERT: D 53 GLN cc_start: 0.8711 (mt0) cc_final: 0.8308 (tt0) REVERT: D 115 ASN cc_start: 0.8555 (m110) cc_final: 0.8245 (m110) REVERT: E 72 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8238 (pp) REVERT: E 112 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7276 (ptp-110) REVERT: E 115 ASN cc_start: 0.8569 (m110) cc_final: 0.8295 (m-40) REVERT: E 148 GLU cc_start: 0.6705 (pm20) cc_final: 0.6304 (pm20) REVERT: F 48 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7854 (mm-30) REVERT: F 223 ASN cc_start: 0.7858 (p0) cc_final: 0.6707 (t0) REVERT: F 224 THR cc_start: 0.9140 (m) cc_final: 0.8828 (t) outliers start: 66 outliers final: 51 residues processed: 296 average time/residue: 0.1390 time to fit residues: 54.5658 Evaluate side-chains 294 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN F 46 HIS ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.082147 restraints weight = 38315.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083937 restraints weight = 22209.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085398 restraints weight = 15264.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086323 restraints weight = 11437.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086935 restraints weight = 9254.421| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.9455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.717 11472 Z= 1.477 Angle : 1.114 31.376 15630 Z= 0.525 Chirality : 0.052 0.312 1830 Planarity : 0.007 0.157 2028 Dihedral : 5.808 55.990 1620 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 5.64 % Allowed : 26.75 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -0.03 (0.21), residues: 1500 helix: 0.49 (0.66), residues: 54 sheet: 0.50 (0.20), residues: 672 loop : -0.48 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 141 TYR 0.018 0.002 TYR B 146 PHE 0.017 0.001 PHE D 60 TRP 0.008 0.001 TRP B 26 HIS 0.022 0.002 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.04258 (11454) covalent geometry : angle 1.11406 (15630) hydrogen bonds : bond 0.04142 ( 360) hydrogen bonds : angle 4.92763 ( 1260) Misc. bond : bond 0.00681 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8376 (tptp) REVERT: A 43 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8162 (tptp) REVERT: A 141 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7511 (ttm-80) REVERT: A 148 GLU cc_start: 0.7183 (pm20) cc_final: 0.6741 (pm20) REVERT: B 43 LYS cc_start: 0.8360 (pttm) cc_final: 0.8033 (ptpt) REVERT: B 53 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7443 (tp40) REVERT: B 99 GLU cc_start: 0.8378 (tt0) cc_final: 0.7956 (tm-30) REVERT: B 100 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.7927 (p) REVERT: B 211 ASP cc_start: 0.8519 (t0) cc_final: 0.8255 (t0) REVERT: B 223 ASN cc_start: 0.7857 (p0) cc_final: 0.7154 (t0) REVERT: C 42 GLU cc_start: 0.8420 (pm20) cc_final: 0.7994 (pm20) REVERT: C 43 LYS cc_start: 0.8654 (pttm) cc_final: 0.8164 (ptpt) REVERT: C 46 HIS cc_start: 0.7809 (t70) cc_final: 0.7526 (t70) REVERT: C 85 TYR cc_start: 0.8797 (m-80) cc_final: 0.8411 (m-80) REVERT: C 148 GLU cc_start: 0.7588 (pp20) cc_final: 0.6709 (pm20) REVERT: C 211 ASP cc_start: 0.8827 (t70) cc_final: 0.8373 (t0) REVERT: D 115 ASN cc_start: 0.8499 (m110) cc_final: 0.8194 (m110) REVERT: E 112 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7218 (ptp-110) REVERT: E 115 ASN cc_start: 0.8638 (m-40) cc_final: 0.8335 (m-40) REVERT: E 148 GLU cc_start: 0.6573 (pm20) cc_final: 0.6229 (pm20) REVERT: F 48 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7802 (mm-30) REVERT: F 188 ARG cc_start: 0.8894 (tpp80) cc_final: 0.8555 (tpp80) outliers start: 66 outliers final: 56 residues processed: 296 average time/residue: 0.1383 time to fit residues: 54.2928 Evaluate side-chains 301 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 57 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN C 53 GLN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082031 restraints weight = 38485.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083826 restraints weight = 22254.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084993 restraints weight = 15196.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085972 restraints weight = 11885.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086772 restraints weight = 9512.001| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.9610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.718 11472 Z= 1.477 Angle : 1.092 30.359 15630 Z= 0.521 Chirality : 0.051 0.315 1830 Planarity : 0.007 0.149 2028 Dihedral : 5.886 54.515 1620 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.15 % Allowed : 27.35 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 aren not related in a simple way. whole: -0.09 (0.21), residues: 1500 helix: 0.75 (0.68), residues: 54 sheet: 0.50 (0.20), residues: 648 loop : -0.56 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 141 TYR 0.020 0.002 TYR B 146 PHE 0.016 0.002 PHE C 60 TRP 0.008 0.001 TRP D 26 HIS 0.026 0.003 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.04259 (11454) covalent geometry : angle 1.09199 (15630) hydrogen bonds : bond 0.04205 ( 360) hydrogen bonds : angle 4.90689 ( 1260) Misc. bond : bond 0.00740 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8400 (tptp) REVERT: A 141 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7465 (ttm-80) REVERT: A 148 GLU cc_start: 0.7189 (pm20) cc_final: 0.6723 (pm20) REVERT: B 25 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8675 (mmmm) REVERT: B 53 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7518 (tp40) REVERT: B 99 GLU cc_start: 0.8381 (tt0) cc_final: 0.7971 (tm-30) REVERT: B 100 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8012 (p) REVERT: B 223 ASN cc_start: 0.7924 (p0) cc_final: 0.7192 (t0) REVERT: C 46 HIS cc_start: 0.7811 (t70) cc_final: 0.7467 (t70) REVERT: C 49 SER cc_start: 0.7885 (t) cc_final: 0.7569 (p) REVERT: C 85 TYR cc_start: 0.8772 (m-80) cc_final: 0.8402 (m-80) REVERT: C 148 GLU cc_start: 0.7668 (pp20) cc_final: 0.6622 (pm20) REVERT: C 211 ASP cc_start: 0.8851 (t70) cc_final: 0.8358 (t0) REVERT: D 115 ASN cc_start: 0.8517 (m110) cc_final: 0.8221 (m110) REVERT: E 112 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7280 (ptp-110) REVERT: E 115 ASN cc_start: 0.8651 (m-40) cc_final: 0.8388 (m-40) REVERT: E 148 GLU cc_start: 0.6594 (pm20) cc_final: 0.6255 (pm20) REVERT: F 48 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7844 (mm-30) REVERT: F 112 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7452 (mmt-90) REVERT: F 188 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8577 (tpp80) outliers start: 72 outliers final: 60 residues processed: 289 average time/residue: 0.1442 time to fit residues: 54.7996 Evaluate side-chains 303 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 GLN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 73 HIS E 254 GLN F 46 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082866 restraints weight = 38062.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084669 restraints weight = 21622.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086061 restraints weight = 14660.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087072 restraints weight = 11028.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087640 restraints weight = 8877.847| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.9783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.717 11472 Z= 1.476 Angle : 1.129 32.037 15630 Z= 0.530 Chirality : 0.052 0.314 1830 Planarity : 0.008 0.150 2028 Dihedral : 5.845 53.149 1620 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.64 % Allowed : 28.38 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 aren not related in a simple way. whole: -0.07 (0.21), residues: 1500 helix: 0.86 (0.70), residues: 54 sheet: 0.52 (0.20), residues: 648 loop : -0.54 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 112 TYR 0.020 0.002 TYR B 85 PHE 0.013 0.001 PHE F 163 TRP 0.030 0.001 TRP B 26 HIS 0.024 0.003 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.04257 (11454) covalent geometry : angle 1.12914 (15630) hydrogen bonds : bond 0.04174 ( 360) hydrogen bonds : angle 4.91159 ( 1260) Misc. bond : bond 0.00793 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7585 (ttm-80) REVERT: A 148 GLU cc_start: 0.7189 (pm20) cc_final: 0.6753 (pm20) REVERT: B 25 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8784 (mmmm) REVERT: B 53 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7460 (tp40) REVERT: B 99 GLU cc_start: 0.8385 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 100 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 148 GLU cc_start: 0.6654 (pm20) cc_final: 0.6329 (pm20) REVERT: B 215 GLU cc_start: 0.8273 (pt0) cc_final: 0.8049 (pm20) REVERT: B 223 ASN cc_start: 0.7942 (p0) cc_final: 0.7197 (t0) REVERT: C 46 HIS cc_start: 0.7778 (t70) cc_final: 0.7428 (t70) REVERT: C 53 GLN cc_start: 0.8541 (mt0) cc_final: 0.8118 (pm20) REVERT: C 85 TYR cc_start: 0.8763 (m-80) cc_final: 0.8347 (m-80) REVERT: C 148 GLU cc_start: 0.7702 (pp20) cc_final: 0.7228 (pm20) REVERT: C 211 ASP cc_start: 0.8842 (t70) cc_final: 0.8454 (t0) REVERT: D 53 GLN cc_start: 0.8956 (mt0) cc_final: 0.8596 (mt0) REVERT: D 115 ASN cc_start: 0.8536 (m110) cc_final: 0.8231 (m110) REVERT: E 60 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7870 (p90) REVERT: E 112 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7230 (ptp-110) REVERT: E 115 ASN cc_start: 0.8666 (m-40) cc_final: 0.8400 (m-40) REVERT: E 148 GLU cc_start: 0.6620 (pm20) cc_final: 0.6268 (pm20) REVERT: F 48 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7791 (mm-30) REVERT: F 112 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7314 (mmt-90) REVERT: F 188 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8628 (tpp80) outliers start: 66 outliers final: 53 residues processed: 279 average time/residue: 0.1390 time to fit residues: 51.5101 Evaluate side-chains 287 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 229 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 GLN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 18 optimal weight: 20.0000 chunk 107 optimal weight: 0.0170 chunk 6 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 0.0370 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 223 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 46 HIS F 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085738 restraints weight = 37802.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087514 restraints weight = 21769.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088777 restraints weight = 14915.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089893 restraints weight = 11583.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090558 restraints weight = 9094.778| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.9846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 1.714 11472 Z= 1.474 Angle : 1.107 29.992 15630 Z= 0.518 Chirality : 0.052 0.316 1830 Planarity : 0.007 0.124 2028 Dihedral : 5.631 52.508 1620 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.62 % Allowed : 29.74 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: 0.08 (0.21), residues: 1500 helix: 0.86 (0.69), residues: 54 sheet: 0.64 (0.20), residues: 648 loop : -0.46 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 112 TYR 0.017 0.001 TYR B 50 PHE 0.017 0.001 PHE C 60 TRP 0.019 0.001 TRP B 26 HIS 0.019 0.002 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.04254 (11454) covalent geometry : angle 1.10704 (15630) hydrogen bonds : bond 0.03796 ( 360) hydrogen bonds : angle 4.89491 ( 1260) Misc. bond : bond 0.00781 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.31 seconds wall clock time: 35 minutes 55.92 seconds (2155.92 seconds total)