Starting phenix.real_space_refine on Sun Dec 29 17:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk8_19264/12_2024/8rk8_19264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk8_19264/12_2024/8rk8_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_19264/12_2024/8rk8_19264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk8_19264/12_2024/8rk8_19264.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk8_19264/12_2024/8rk8_19264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk8_19264/12_2024/8rk8_19264.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, F Time building chain proxies: 4.29, per 1000 atoms: 0.38 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.72 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: 3.35 Time building geometry restraints manager: 3.61 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: 0.00 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.570 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- 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 : 0.003 0.084 11454 Z= 0.219 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP C 28 HIS 0.001 0.000 HIS E 46 PHE 0.007 0.001 PHE F 60 TYR 0.011 0.001 TYR E 169 ARG 0.001 0.000 ARG C 188 *********************** 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 : 1.348 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: 0.6426 (tm-30) REVERT: C 182 GLN cc_start: 0.7457 (tt0) cc_final: 0.7013 (tt0) REVERT: D 47 LYS cc_start: 0.7645 (mttm) cc_final: 0.7309 (pptt) REVERT: D 71 THR cc_start: 0.8201 (m) cc_final: 0.7769 (m) REVERT: D 163 PHE cc_start: 0.7261 (m-10) cc_final: 0.6894 (m-10) REVERT: D 219 ILE cc_start: 0.7973 (mt) cc_final: 0.7691 (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: 0.2678 time to fit residues: 199.4618 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 : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.0060 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 B 79 ASN C 38 GLN C 79 ASN C 136 GLN C 182 GLN D 79 ASN E 79 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.718 11454 Z= 3.479 Angle : 1.107 26.186 15630 Z= 0.546 Chirality : 0.054 0.242 1830 Planarity : 0.008 0.079 2028 Dihedral : 5.328 21.209 1620 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.98 % Allowed : 16.07 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1500 helix: 0.27 (0.70), residues: 54 sheet: 0.27 (0.20), residues: 660 loop : -0.08 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP F 26 HIS 0.008 0.002 HIS A 46 PHE 0.030 0.003 PHE D 60 TYR 0.026 0.003 TYR D 50 ARG 0.009 0.001 ARG F 27 *********************** 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 430 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 360 time to evaluate : 1.380 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 211 ASP cc_start: 0.8403 (t0) cc_final: 0.8159 (t0) REVERT: B 99 GLU cc_start: 0.7521 (tt0) cc_final: 0.7154 (tm-30) REVERT: B 211 ASP cc_start: 0.8239 (t0) cc_final: 0.7957 (t0) REVERT: C 163 PHE cc_start: 0.7371 (m-80) cc_final: 0.7143 (m-80) REVERT: D 47 LYS cc_start: 0.8299 (mttm) cc_final: 0.7298 (pptt) REVERT: D 223 ASN cc_start: 0.5358 (t0) cc_final: 0.5143 (t0) REVERT: F 112 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7576 (ptp-110) REVERT: F 148 GLU cc_start: 0.5889 (pm20) cc_final: 0.5620 (pm20) REVERT: F 223 ASN cc_start: 0.6201 (p0) cc_final: 0.5910 (t0) outliers start: 70 outliers final: 37 residues processed: 390 average time/residue: 0.2940 time to fit residues: 153.4668 Evaluate side-chains 330 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 133 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 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 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 96 VAL 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 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.0020 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 0.0020 chunk 109 optimal weight: 8.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 223 ASN B 136 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN D 53 GLN D 73 HIS D 136 GLN ** E 79 ASN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.729 11454 Z= 3.479 Angle : 1.063 27.085 15630 Z= 0.517 Chirality : 0.052 0.235 1830 Planarity : 0.008 0.147 2028 Dihedral : 5.458 22.125 1620 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 6.92 % Allowed : 18.29 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1500 helix: -0.43 (0.67), residues: 54 sheet: 0.55 (0.19), residues: 744 loop : -0.20 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 26 HIS 0.015 0.002 HIS A 46 PHE 0.026 0.002 PHE D 60 TYR 0.018 0.002 TYR B 85 ARG 0.008 0.001 ARG A 112 *********************** 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 381 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 1.255 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: B 99 GLU cc_start: 0.7824 (tt0) cc_final: 0.7323 (tm-30) REVERT: D 26 TRP cc_start: 0.7271 (m100) cc_final: 0.6951 (m100) REVERT: E 112 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7144 (ptp-110) REVERT: F 112 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7721 (ptp-110) REVERT: F 148 GLU cc_start: 0.6123 (pm20) cc_final: 0.5745 (pm20) REVERT: F 223 ASN cc_start: 0.6690 (p0) cc_final: 0.6220 (t0) outliers start: 81 outliers final: 46 residues processed: 345 average time/residue: 0.3081 time to fit residues: 140.1171 Evaluate side-chains 299 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 ILE 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 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 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 133 LEU 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 67 THR 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 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 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 216 LEU Chi-restraints excluded: chain E residue 224 THR 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 84 LEU Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 177 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.716 11454 Z= 3.463 Angle : 1.034 28.368 15630 Z= 0.495 Chirality : 0.050 0.213 1830 Planarity : 0.008 0.153 2028 Dihedral : 5.206 29.039 1620 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.47 % Allowed : 21.71 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1500 helix: 0.03 (0.67), residues: 54 sheet: 0.68 (0.21), residues: 600 loop : -0.11 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 26 HIS 0.003 0.001 HIS A 46 PHE 0.019 0.002 PHE A 60 TYR 0.025 0.002 TYR C 206 ARG 0.026 0.002 ARG B 112 *********************** 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 365 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 1.331 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: A 54 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7834 (mttt) REVERT: A 236 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 49 SER cc_start: 0.6026 (t) cc_final: 0.5761 (p) REVERT: B 99 GLU cc_start: 0.7653 (tt0) cc_final: 0.7261 (tm-30) REVERT: D 47 LYS cc_start: 0.8707 (mttm) cc_final: 0.7594 (pptt) REVERT: E 38 GLN cc_start: 0.7412 (mp10) cc_final: 0.7157 (mp10) REVERT: E 48 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7264 (mm-30) REVERT: E 112 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7049 (ptp-110) REVERT: E 148 GLU cc_start: 0.5987 (pm20) cc_final: 0.5749 (pm20) REVERT: F 112 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7566 (ptp-110) REVERT: F 223 ASN cc_start: 0.6706 (p0) cc_final: 0.6350 (t0) outliers start: 64 outliers final: 39 residues processed: 334 average time/residue: 0.3120 time to fit residues: 136.5815 Evaluate side-chains 298 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 175 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 133 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 36 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 51 SER 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 213 LEU Chi-restraints excluded: chain D residue 230 ILE 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 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 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 54 LYS Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 215 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 79 ASN B 254 GLN C 79 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.8455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.721 11454 Z= 3.475 Angle : 1.141 32.636 15630 Z= 0.539 Chirality : 0.051 0.196 1830 Planarity : 0.007 0.083 2028 Dihedral : 5.649 34.083 1620 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.92 % Allowed : 22.05 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1500 helix: 0.25 (0.68), residues: 54 sheet: 0.46 (0.21), residues: 666 loop : -0.17 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 26 HIS 0.022 0.003 HIS A 46 PHE 0.017 0.002 PHE D 60 TYR 0.020 0.002 TYR B 146 ARG 0.011 0.002 ARG C 58 *********************** 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 350 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 1.317 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: A 54 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7920 (mttt) REVERT: A 207 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8281 (ttpt) REVERT: B 99 GLU cc_start: 0.7847 (tt0) cc_final: 0.7438 (tm-30) REVERT: D 79 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8412 (m110) REVERT: D 115 ASN cc_start: 0.8412 (m110) cc_final: 0.8193 (m-40) REVERT: E 48 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 112 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7442 (ptp-110) REVERT: E 148 GLU cc_start: 0.6178 (pm20) cc_final: 0.5872 (pm20) REVERT: F 112 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7877 (ptp-110) REVERT: F 223 ASN cc_start: 0.6983 (p0) cc_final: 0.6350 (t0) REVERT: F 224 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8197 (t) outliers start: 81 outliers final: 60 residues processed: 314 average time/residue: 0.2983 time to fit residues: 123.9631 Evaluate side-chains 314 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 70 ILE 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 B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 ASN 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 65 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 SER 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 51 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 ASN 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 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 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 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 44 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 139 optimal weight: 40.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 254 GLN D 46 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN F 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.8734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.716 11454 Z= 3.463 Angle : 1.115 32.081 15630 Z= 0.525 Chirality : 0.051 0.198 1830 Planarity : 0.006 0.077 2028 Dihedral : 5.417 46.944 1620 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.47 % Allowed : 24.79 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1500 helix: 0.14 (0.66), residues: 54 sheet: 0.67 (0.20), residues: 672 loop : -0.27 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 26 HIS 0.009 0.001 HIS A 46 PHE 0.019 0.001 PHE D 60 TYR 0.017 0.002 TYR B 146 ARG 0.008 0.001 ARG C 58 *********************** 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 329 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 1.332 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: A 54 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8075 (mttt) REVERT: B 99 GLU cc_start: 0.7802 (tt0) cc_final: 0.7454 (tm-30) REVERT: D 115 ASN cc_start: 0.8405 (m110) cc_final: 0.8188 (m110) REVERT: E 112 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7431 (ptp-110) REVERT: E 148 GLU cc_start: 0.5968 (pm20) cc_final: 0.5734 (pm20) REVERT: F 112 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7546 (ptp-110) REVERT: F 223 ASN cc_start: 0.6826 (p0) cc_final: 0.6354 (t0) outliers start: 64 outliers final: 44 residues processed: 305 average time/residue: 0.2993 time to fit residues: 120.8322 Evaluate side-chains 290 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 254 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 190 LYS 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 65 THR Chi-restraints excluded: chain C residue 67 THR 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 33 SER 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 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 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 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 215 GLU 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 16 optimal weight: 8.9990 chunk 82 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 chunk 88 optimal weight: 0.0070 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 57 optimal weight: 7.9990 overall best weight: 2.4218 ------------------------------------------------------------------------------- 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 254 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.9025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.719 11454 Z= 3.467 Angle : 1.177 38.842 15630 Z= 0.544 Chirality : 0.051 0.199 1830 Planarity : 0.006 0.076 2028 Dihedral : 5.458 40.165 1620 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.73 % Allowed : 25.13 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1500 helix: 0.53 (0.68), residues: 54 sheet: 0.65 (0.20), residues: 672 loop : -0.31 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 26 HIS 0.010 0.002 HIS A 46 PHE 0.019 0.002 PHE D 60 TYR 0.020 0.002 TYR B 50 ARG 0.012 0.001 ARG A 141 *********************** 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 322 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 1.369 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: A 141 ARG cc_start: 0.7370 (ttm110) cc_final: 0.7141 (ttm-80) REVERT: B 99 GLU cc_start: 0.7869 (tt0) cc_final: 0.7524 (tm-30) REVERT: B 100 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7751 (p) REVERT: D 115 ASN cc_start: 0.8461 (m110) cc_final: 0.8246 (m110) REVERT: E 112 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7570 (ptp-110) REVERT: E 141 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7691 (ttp80) REVERT: F 112 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7567 (ptp-110) REVERT: F 204 GLU cc_start: 0.6331 (mm-30) cc_final: 0.6067 (mm-30) REVERT: F 223 ASN cc_start: 0.6666 (p0) cc_final: 0.6263 (t0) outliers start: 67 outliers final: 50 residues processed: 294 average time/residue: 0.3064 time to fit residues: 119.0046 Evaluate side-chains 291 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 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 245 ASP Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 ASN 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 46 HIS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 133 LEU 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 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 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 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 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 215 GLU 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 86 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 79 ASN B 254 GLN C 254 GLN D 46 HIS D 53 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.9382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.721 11454 Z= 3.474 Angle : 1.135 28.944 15630 Z= 0.552 Chirality : 0.051 0.272 1830 Planarity : 0.006 0.079 2028 Dihedral : 5.954 55.710 1620 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.73 % Allowed : 25.73 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1500 helix: 0.57 (0.68), residues: 54 sheet: 0.66 (0.20), residues: 678 loop : -0.51 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 26 HIS 0.012 0.002 HIS D 46 PHE 0.013 0.002 PHE F 163 TYR 0.021 0.002 TYR B 146 ARG 0.010 0.002 ARG A 141 *********************** 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 319 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 1.253 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: B 54 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7326 (mmmt) REVERT: B 99 GLU cc_start: 0.7943 (tt0) cc_final: 0.7650 (tm-30) REVERT: B 100 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7863 (p) REVERT: B 211 ASP cc_start: 0.7770 (t70) cc_final: 0.7476 (t0) REVERT: C 211 ASP cc_start: 0.7914 (t70) cc_final: 0.7523 (t0) REVERT: C 243 THR cc_start: 0.7638 (p) cc_final: 0.7436 (t) REVERT: D 115 ASN cc_start: 0.8510 (m110) cc_final: 0.8288 (m110) REVERT: E 112 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7683 (ptp-110) REVERT: E 148 GLU cc_start: 0.6197 (pm20) cc_final: 0.5705 (pm20) REVERT: F 25 LYS cc_start: 0.7836 (tptp) cc_final: 0.7540 (mmmt) outliers start: 67 outliers final: 56 residues processed: 294 average time/residue: 0.3040 time to fit residues: 117.8136 Evaluate side-chains 283 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 224 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 245 ASP Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 ASN 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 46 HIS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 133 LEU 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 50 TYR Chi-restraints excluded: chain D residue 57 VAL 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 112 ARG Chi-restraints excluded: chain D residue 128 SER 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 32 VAL 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 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 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 215 GLU Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.9639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.718 11454 Z= 3.468 Angle : 1.161 31.831 15630 Z= 0.555 Chirality : 0.051 0.208 1830 Planarity : 0.006 0.109 2028 Dihedral : 6.026 62.833 1620 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.21 % Allowed : 27.18 % Favored : 67.61 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1500 helix: 0.52 (0.67), residues: 54 sheet: 0.72 (0.20), residues: 672 loop : -0.61 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 26 HIS 0.013 0.002 HIS A 46 PHE 0.015 0.001 PHE D 60 TYR 0.021 0.002 TYR B 146 ARG 0.012 0.001 ARG F 112 *********************** 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 311 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 250 time to evaluate : 1.291 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: B 54 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7532 (mmmt) REVERT: B 99 GLU cc_start: 0.7932 (tt0) cc_final: 0.7675 (tm-30) REVERT: B 100 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7865 (p) REVERT: C 211 ASP cc_start: 0.7903 (t70) cc_final: 0.7494 (t0) REVERT: D 115 ASN cc_start: 0.8508 (m110) cc_final: 0.8295 (m110) REVERT: E 112 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7613 (ptp-110) REVERT: E 148 GLU cc_start: 0.6130 (pm20) cc_final: 0.5650 (pm20) REVERT: F 25 LYS cc_start: 0.7813 (tptp) cc_final: 0.7561 (mmmt) outliers start: 61 outliers final: 53 residues processed: 287 average time/residue: 0.3106 time to fit residues: 117.9094 Evaluate side-chains 289 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 54 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 ASN 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 46 HIS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 133 LEU 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 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 67 THR 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 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain E residue 32 VAL 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 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 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 79 ASN ** B 182 GLN ** 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 ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.9890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.724 11454 Z= 3.484 Angle : 1.275 38.117 15630 Z= 0.604 Chirality : 0.052 0.277 1830 Planarity : 0.007 0.082 2028 Dihedral : 6.461 53.198 1620 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.30 % Allowed : 27.78 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1500 helix: 0.38 (0.68), residues: 54 sheet: 0.44 (0.20), residues: 696 loop : -0.79 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 26 HIS 0.007 0.002 HIS F 46 PHE 0.016 0.002 PHE D 60 TYR 0.027 0.002 TYR B 146 ARG 0.011 0.002 ARG B 58 ********************** 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 291 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.199 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: B 54 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7923 (mmmt) REVERT: B 100 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 211 ASP cc_start: 0.7862 (t70) cc_final: 0.7447 (t0) REVERT: C 211 ASP cc_start: 0.7972 (t70) cc_final: 0.7611 (t0) REVERT: D 115 ASN cc_start: 0.8603 (m110) cc_final: 0.8396 (m110) REVERT: E 112 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7629 (ptp-110) REVERT: E 141 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7799 (ttp80) outliers start: 62 outliers final: 57 residues processed: 269 average time/residue: 0.3027 time to fit residues: 107.6037 Evaluate side-chains 276 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 54 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 80 LEU 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 46 HIS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 133 LEU 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 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 54 LYS 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 112 ARG Chi-restraints excluded: chain D residue 128 SER 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 32 VAL 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 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 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 0.0370 chunk 21 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083767 restraints weight = 37905.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085561 restraints weight = 21853.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086896 restraints weight = 14962.774| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.9960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.717 11454 Z= 3.466 Angle : 1.184 34.873 15630 Z= 0.558 Chirality : 0.052 0.394 1830 Planarity : 0.006 0.082 2028 Dihedral : 5.978 51.556 1620 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.27 % Allowed : 29.23 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1500 helix: 0.38 (0.68), residues: 54 sheet: 0.67 (0.21), residues: 588 loop : -0.73 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 26 HIS 0.022 0.002 HIS D 46 PHE 0.022 0.001 PHE F 60 TYR 0.027 0.002 TYR B 146 ARG 0.009 0.001 ARG F 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.63 seconds wall clock time: 55 minutes 41.98 seconds (3341.98 seconds total)