Starting phenix.real_space_refine on Sat Oct 12 00:47:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk8_19264/10_2024/8rk8_19264.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk8_19264/10_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk8_19264/10_2024/8rk8_19264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk8_19264/10_2024/8rk8_19264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk8_19264/10_2024/8rk8_19264.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk8_19264/10_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-5477/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: 4.32, 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=0, symmetry=0 Time building additional restraints: 2.87 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: 1.71 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: 3.62 Time building geometry restraints manager: 3.31 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: 0.48 - 1.36: 138 1.36 - 2.25: 252 2.25 - 3.13: 8679 3.13 - 4.02: 26568 4.02 - 4.90: 49659 Warning: very small nonbonded interaction distances. Nonbonded interactions: 85296 Sorted by model distance: nonbonded pdb=" NZ LYS C 87 " pdb=" CG ASP D 245 " model vdw 0.476 3.350 nonbonded pdb=" CG ASP A 245 " pdb=" NZ LYS F 87 " model vdw 0.476 3.350 nonbonded pdb=" NZ LYS A 87 " pdb=" CG ASP B 245 " model vdw 0.476 3.350 nonbonded pdb=" NZ LYS B 87 " pdb=" CG ASP C 245 " model vdw 0.476 3.350 nonbonded pdb=" NZ LYS E 87 " pdb=" CG ASP F 245 " model vdw 0.476 3.350 ... (remaining 85291 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 25.840 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- 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= 0.194 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 : 0.476 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 fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 1.296 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: 0.2654 time to fit residues: 197.5185 Evaluate side-chains 324 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 79 ASN A 174 GLN A 223 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 38 GLN C 79 ASN C 136 GLN C 182 GLN D 20 ASN D 79 ASN ** 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: 0.7253 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.713 11454 Z= 2.781 Angle : 1.077 26.125 15630 Z= 0.528 Chirality : 0.054 0.225 1830 Planarity : 0.007 0.077 2028 Dihedral : 5.190 22.529 1620 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.15 % Allowed : 15.21 % Favored : 78.63 % 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: 0.09 (0.22), residues: 1500 helix: 0.39 (0.69), residues: 54 sheet: 0.25 (0.20), residues: 720 loop : -0.02 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 26 HIS 0.008 0.002 HIS A 46 PHE 0.026 0.002 PHE D 60 TYR 0.024 0.003 TYR B 169 ARG 0.013 0.002 ARG C 112 *********************** 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 432 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 360 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 211 ASP cc_start: 0.8435 (t0) cc_final: 0.8218 (t0) REVERT: B 99 GLU cc_start: 0.7466 (tt0) cc_final: 0.7001 (tm-30) REVERT: B 211 ASP cc_start: 0.8203 (t0) cc_final: 0.7800 (t0) REVERT: C 99 GLU cc_start: 0.6978 (tt0) cc_final: 0.6651 (tm-30) REVERT: C 163 PHE cc_start: 0.7353 (m-80) cc_final: 0.7059 (m-80) REVERT: D 192 ILE cc_start: 0.8434 (mm) cc_final: 0.8114 (mt) REVERT: D 223 ASN cc_start: 0.5188 (t0) cc_final: 0.4969 (t0) REVERT: E 89 VAL cc_start: 0.7955 (p) cc_final: 0.7653 (m) REVERT: E 223 ASN cc_start: 0.5819 (p0) cc_final: 0.5545 (t0) REVERT: F 43 LYS cc_start: 0.7285 (pttm) cc_final: 0.7022 (pttm) REVERT: F 223 ASN cc_start: 0.6048 (p0) cc_final: 0.5677 (t0) outliers start: 72 outliers final: 38 residues processed: 394 average time/residue: 0.2839 time to fit residues: 149.1077 Evaluate side-chains 333 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 294 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 89 VAL 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 25 LYS 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 D residue 19 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 31 ASP 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 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 44 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 149 VAL 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: 5.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 254 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 254 GLN D 20 ASN D 73 HIS D 136 GLN E 79 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.740 11454 Z= 2.810 Angle : 1.061 27.077 15630 Z= 0.526 Chirality : 0.053 0.192 1830 Planarity : 0.007 0.066 2028 Dihedral : 5.737 22.506 1620 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 7.44 % Allowed : 18.38 % Favored : 74.19 % 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: 0.15 (0.21), residues: 1500 helix: -0.46 (0.66), residues: 54 sheet: 0.55 (0.20), residues: 672 loop : -0.18 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 28 HIS 0.032 0.004 HIS A 46 PHE 0.012 0.002 PHE F 163 TYR 0.024 0.003 TYR B 85 ARG 0.015 0.001 ARG A 58 *********************** 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 392 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 305 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7287 (t70) REVERT: B 49 SER cc_start: 0.6286 (t) cc_final: 0.6055 (p) REVERT: B 54 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6377 (pttt) REVERT: B 99 GLU cc_start: 0.7998 (tt0) cc_final: 0.7642 (tm-30) REVERT: D 115 ASN cc_start: 0.8365 (m110) cc_final: 0.8144 (m110) REVERT: D 211 ASP cc_start: 0.7673 (t0) cc_final: 0.7253 (t0) REVERT: E 48 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7252 (mm-30) REVERT: E 112 ARG cc_start: 0.8734 (ptp-110) cc_final: 0.8382 (ptp-110) REVERT: E 148 GLU cc_start: 0.6202 (pm20) cc_final: 0.5886 (pm20) REVERT: F 43 LYS cc_start: 0.7568 (pttm) cc_final: 0.7356 (pttm) REVERT: F 223 ASN cc_start: 0.6836 (p0) cc_final: 0.6324 (t0) REVERT: F 224 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8188 (t) outliers start: 87 outliers final: 52 residues processed: 354 average time/residue: 0.3113 time to fit residues: 144.0091 Evaluate side-chains 288 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 235 LEU Chi-restraints excluded: chain A residue 245 ASP 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 79 ASN Chi-restraints excluded: chain B residue 110 VAL 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 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 35 MET 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 89 VAL 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 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 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 111 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 216 LEU 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 60 PHE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 84 LEU 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: 0.5980 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 39 optimal weight: 50.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN E 79 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 HIS F 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.8658 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= 2.783 Angle : 0.992 28.308 15630 Z= 0.482 Chirality : 0.051 0.163 1830 Planarity : 0.006 0.079 2028 Dihedral : 5.155 20.414 1620 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.98 % Allowed : 22.48 % Favored : 71.54 % 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: 0.15 (0.66), residues: 54 sheet: 0.68 (0.20), residues: 660 loop : -0.18 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 26 HIS 0.003 0.001 HIS F 46 PHE 0.020 0.002 PHE D 60 TYR 0.023 0.002 TYR C 206 ARG 0.015 0.002 ARG A 58 *********************** 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 360 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 1.160 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: B 49 SER cc_start: 0.6186 (t) cc_final: 0.5963 (p) REVERT: B 99 GLU cc_start: 0.7863 (tt0) cc_final: 0.7528 (tm-30) REVERT: D 62 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8293 (pt) REVERT: D 79 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8458 (m110) REVERT: D 115 ASN cc_start: 0.8373 (m110) cc_final: 0.8154 (m110) REVERT: E 112 ARG cc_start: 0.8676 (ptp-110) cc_final: 0.8270 (ptp-110) REVERT: E 141 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7543 (ttp80) REVERT: F 43 LYS cc_start: 0.7316 (pttm) cc_final: 0.7048 (pttm) REVERT: F 223 ASN cc_start: 0.6891 (p0) cc_final: 0.6392 (t0) REVERT: F 255 LEU cc_start: 0.8860 (tp) cc_final: 0.8553 (mm) outliers start: 70 outliers final: 42 residues processed: 332 average time/residue: 0.3125 time to fit residues: 135.8847 Evaluate side-chains 292 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 248 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 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 60 PHE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 82 LEU 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 33 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 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 111 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 235 LEU 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: 7.9990 chunk 2 optimal weight: 0.2980 chunk 107 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.2764 ------------------------------------------------------------------------------- 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 ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 46 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.9044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.722 11454 Z= 2.778 Angle : 0.990 29.063 15630 Z= 0.479 Chirality : 0.050 0.174 1830 Planarity : 0.005 0.062 2028 Dihedral : 5.273 20.999 1620 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.98 % Allowed : 24.36 % Favored : 69.66 % 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: 0.17 (0.21), residues: 1500 helix: 0.02 (0.67), residues: 54 sheet: 0.66 (0.20), residues: 660 loop : -0.30 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.016 0.002 HIS A 46 PHE 0.027 0.002 PHE D 60 TYR 0.018 0.002 TYR B 146 ARG 0.010 0.001 ARG F 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 353 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 283 time to evaluate : 1.194 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 49 SER cc_start: 0.6430 (t) cc_final: 0.6194 (p) REVERT: B 99 GLU cc_start: 0.7853 (tt0) cc_final: 0.7570 (tm-30) REVERT: C 211 ASP cc_start: 0.7850 (t0) cc_final: 0.7406 (t0) REVERT: D 115 ASN cc_start: 0.8411 (m110) cc_final: 0.8172 (m110) REVERT: E 45 GLU cc_start: 0.7999 (pt0) cc_final: 0.7750 (pt0) REVERT: E 112 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8295 (ptp-110) REVERT: F 223 ASN cc_start: 0.6675 (p0) cc_final: 0.6302 (t0) REVERT: F 255 LEU cc_start: 0.8891 (tp) cc_final: 0.8668 (mm) outliers start: 70 outliers final: 53 residues processed: 330 average time/residue: 0.3069 time to fit residues: 132.1834 Evaluate side-chains 297 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU 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 67 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 82 LEU 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 C residue 213 LEU 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 51 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 68 VAL 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 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ASN 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: 5.9990 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 chunk 139 optimal weight: 50.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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 223 ASN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 254 GLN D 46 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 46 HIS F 79 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.9517 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= 2.789 Angle : 0.996 28.499 15630 Z= 0.483 Chirality : 0.051 0.168 1830 Planarity : 0.005 0.063 2028 Dihedral : 5.410 22.040 1620 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 7.09 % Allowed : 25.21 % Favored : 67.69 % 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: -0.09 (0.21), residues: 1500 helix: 0.09 (0.65), residues: 54 sheet: 0.63 (0.20), residues: 624 loop : -0.59 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 26 HIS 0.018 0.002 HIS A 46 PHE 0.026 0.002 PHE F 60 TYR 0.016 0.002 TYR F 50 ARG 0.009 0.001 ARG E 27 *********************** 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 354 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 271 time to evaluate : 1.313 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: B 54 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6092 (pttt) REVERT: C 211 ASP cc_start: 0.7895 (t0) cc_final: 0.7475 (t0) REVERT: D 79 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8509 (m110) REVERT: D 115 ASN cc_start: 0.8434 (m110) cc_final: 0.8204 (m110) REVERT: D 246 LEU cc_start: 0.7468 (pt) cc_final: 0.7134 (pp) REVERT: E 112 ARG cc_start: 0.8774 (ptp-110) cc_final: 0.8395 (ptp-110) outliers start: 83 outliers final: 64 residues processed: 324 average time/residue: 0.2910 time to fit residues: 124.5643 Evaluate side-chains 301 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 235 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 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 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 33 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 45 GLU 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 128 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 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 68 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 254 GLN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ASN 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: 5.9990 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 223 ASN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 46 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.9657 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= 2.779 Angle : 0.985 28.584 15630 Z= 0.475 Chirality : 0.050 0.172 1830 Planarity : 0.005 0.060 2028 Dihedral : 5.153 19.978 1620 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.07 % Allowed : 27.26 % Favored : 66.67 % 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: -0.00 (0.21), residues: 1500 helix: 0.14 (0.67), residues: 54 sheet: 0.69 (0.20), residues: 624 loop : -0.53 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 26 HIS 0.015 0.002 HIS F 46 PHE 0.023 0.002 PHE F 60 TYR 0.016 0.002 TYR B 146 ARG 0.009 0.001 ARG F 27 *********************** 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 336 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 265 time to evaluate : 1.318 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 54 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.5979 (pttt) REVERT: C 43 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7134 (ptmt) REVERT: C 211 ASP cc_start: 0.7818 (t0) cc_final: 0.7415 (t0) REVERT: D 115 ASN cc_start: 0.8402 (m110) cc_final: 0.8171 (m110) REVERT: E 112 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8273 (ptp-110) REVERT: F 99 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7824 (tm-30) outliers start: 71 outliers final: 52 residues processed: 309 average time/residue: 0.2912 time to fit residues: 119.6038 Evaluate side-chains 305 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 252 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 32 VAL 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 213 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 79 ASN 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: 0.6980 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 223 ASN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 1.0034 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= 2.798 Angle : 1.034 28.564 15630 Z= 0.504 Chirality : 0.051 0.182 1830 Planarity : 0.005 0.061 2028 Dihedral : 5.591 23.262 1620 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.84 % Allowed : 27.44 % Favored : 65.73 % 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: -0.34 (0.21), residues: 1500 helix: -0.34 (0.67), residues: 54 sheet: 0.53 (0.20), residues: 624 loop : -0.81 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 28 HIS 0.015 0.002 HIS A 46 PHE 0.019 0.002 PHE D 60 TYR 0.017 0.002 TYR B 146 ARG 0.009 0.001 ARG F 27 *********************** 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 311 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 231 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6082 (pttt) REVERT: C 211 ASP cc_start: 0.7937 (t70) cc_final: 0.7563 (t0) REVERT: D 79 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8470 (m110) REVERT: D 115 ASN cc_start: 0.8507 (m110) cc_final: 0.8266 (m110) REVERT: D 211 ASP cc_start: 0.8207 (t70) cc_final: 0.7623 (t0) REVERT: E 112 ARG cc_start: 0.8817 (ptp-110) cc_final: 0.8539 (ptp-110) REVERT: F 246 LEU cc_start: 0.8196 (pt) cc_final: 0.7816 (pp) outliers start: 80 outliers final: 65 residues processed: 286 average time/residue: 0.2923 time to fit residues: 111.5467 Evaluate side-chains 289 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 222 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 32 VAL 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 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 68 VAL 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 128 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 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 59 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 225 VAL 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: 8.9990 chunk 138 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 53 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 46 HIS E 161 GLN F 46 HIS F 79 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 1.0081 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= 2.781 Angle : 1.001 28.791 15630 Z= 0.484 Chirality : 0.051 0.167 1830 Planarity : 0.005 0.059 2028 Dihedral : 5.183 20.351 1620 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.44 % Allowed : 30.43 % Favored : 65.13 % 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: -0.15 (0.21), residues: 1500 helix: -0.19 (0.68), residues: 54 sheet: 0.67 (0.20), residues: 624 loop : -0.69 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 26 HIS 0.010 0.002 HIS A 46 PHE 0.022 0.001 PHE D 60 TYR 0.018 0.002 TYR B 146 ARG 0.016 0.002 ARG D 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 319 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 267 time to evaluate : 1.289 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: B 54 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6073 (pttt) REVERT: B 148 GLU cc_start: 0.6518 (pm20) cc_final: 0.6274 (pm20) REVERT: C 211 ASP cc_start: 0.7814 (t70) cc_final: 0.7444 (t0) REVERT: D 115 ASN cc_start: 0.8435 (m110) cc_final: 0.8182 (m110) REVERT: D 211 ASP cc_start: 0.8015 (t70) cc_final: 0.7653 (t0) REVERT: E 64 LYS cc_start: 0.7174 (mptt) cc_final: 0.6632 (mttp) REVERT: E 112 ARG cc_start: 0.8652 (ptp-110) cc_final: 0.8238 (ptp-110) REVERT: F 246 LEU cc_start: 0.7946 (pt) cc_final: 0.7520 (pp) outliers start: 52 outliers final: 40 residues processed: 301 average time/residue: 0.3268 time to fit residues: 129.1130 Evaluate side-chains 281 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 106 VAL 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 44 VAL Chi-restraints excluded: chain E residue 46 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 177 MET 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: 0.0000 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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 B 79 ASN B 223 ASN B 254 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS F 46 HIS F 79 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 1.0263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.723 11454 Z= 2.792 Angle : 1.037 29.462 15630 Z= 0.503 Chirality : 0.051 0.177 1830 Planarity : 0.006 0.130 2028 Dihedral : 5.459 21.832 1620 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.62 % Allowed : 30.51 % Favored : 64.87 % 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: -0.30 (0.21), residues: 1500 helix: -0.42 (0.67), residues: 54 sheet: 0.39 (0.20), residues: 672 loop : -0.68 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 26 HIS 0.008 0.002 HIS D 46 PHE 0.025 0.002 PHE C 60 TYR 0.023 0.002 TYR B 146 ARG 0.026 0.002 ARG D 112 ********************** 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 283 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 229 time to evaluate : 1.345 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: B 54 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6073 (pttt) REVERT: B 148 GLU cc_start: 0.6552 (pm20) cc_final: 0.6217 (pm20) REVERT: C 211 ASP cc_start: 0.7883 (t70) cc_final: 0.7543 (t0) REVERT: D 115 ASN cc_start: 0.8526 (m110) cc_final: 0.8280 (m110) REVERT: D 211 ASP cc_start: 0.8158 (t70) cc_final: 0.7541 (t0) REVERT: E 112 ARG cc_start: 0.8755 (ptp-110) cc_final: 0.8450 (ptp-110) REVERT: F 246 LEU cc_start: 0.8140 (pt) cc_final: 0.7729 (pp) outliers start: 54 outliers final: 46 residues processed: 265 average time/residue: 0.3101 time to fit residues: 107.6347 Evaluate side-chains 265 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 106 VAL 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 59 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 225 VAL 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: 6.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN B 79 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS F 46 HIS F 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076261 restraints weight = 38786.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077911 restraints weight = 21773.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079110 restraints weight = 14811.884| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 1.0374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.723 11454 Z= 2.799 Angle : 1.059 30.484 15630 Z= 0.516 Chirality : 0.052 0.185 1830 Planarity : 0.006 0.111 2028 Dihedral : 5.658 23.131 1620 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.87 % Allowed : 30.26 % Favored : 64.87 % 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: -0.51 (0.21), residues: 1500 helix: -0.66 (0.64), residues: 54 sheet: 0.30 (0.20), residues: 672 loop : -0.87 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 26 HIS 0.011 0.002 HIS F 46 PHE 0.024 0.002 PHE C 60 TYR 0.024 0.002 TYR A 50 ARG 0.018 0.002 ARG C 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.11 seconds wall clock time: 54 minutes 16.95 seconds (3256.95 seconds total)