Starting phenix.real_space_refine on Tue Mar 3 22:03:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nhv_9374/03_2026/6nhv_9374.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nhv_9374/03_2026/6nhv_9374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nhv_9374/03_2026/6nhv_9374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nhv_9374/03_2026/6nhv_9374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nhv_9374/03_2026/6nhv_9374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nhv_9374/03_2026/6nhv_9374.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.934 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 31 5.16 5 C 5653 2.51 5 N 1546 2.21 5 O 1718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "A" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1358 Unusual residues: {'CRO': 1} Classifications: {'peptide': 165, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158, None: 1} Not linked: pdbres="CRO A 66 " pdbres="VAL A 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "R" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2251 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 290} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1107 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1107 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "X" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 8948 At special positions: 0 Unit cell: (119.78, 94.34, 115.54, 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 31 16.00 O 1718 8.00 N 1546 7.00 C 5653 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 276.7 milliseconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 51.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.701A pdb=" N THR A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 75 through 81 removed outlier: 5.435A pdb=" N ARG A 80 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'N' and resid 17 through 31 removed outlier: 3.737A pdb=" N LEU N 22 " --> pdb=" O PRO N 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU N 23 " --> pdb=" O GLY N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 89 removed outlier: 3.748A pdb=" N ALA N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 31 removed outlier: 3.707A pdb=" N LEU O 22 " --> pdb=" O PRO O 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU O 23 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 89 removed outlier: 3.820A pdb=" N ALA O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 45 removed outlier: 3.581A pdb=" N SER R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 40 " --> pdb=" O GLU R 36 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY R 42 " --> pdb=" O THR R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 72 removed outlier: 3.628A pdb=" N GLU R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY R 68 " --> pdb=" O TYR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 98 removed outlier: 4.091A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU R 88 " --> pdb=" O ILE R 84 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 137 removed outlier: 3.581A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR R 131 " --> pdb=" O ARG R 127 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 175 removed outlier: 3.625A pdb=" N TYR R 145 " --> pdb=" O GLU R 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 162 " --> pdb=" O ARG R 158 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS R 167 " --> pdb=" O GLU R 163 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU R 168 " --> pdb=" O GLN R 164 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 186 removed outlier: 3.789A pdb=" N VAL R 180 " --> pdb=" O GLN R 176 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 208 Processing helix chain 'R' and resid 209 through 220 removed outlier: 3.711A pdb=" N CYS R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 242 through 252 removed outlier: 3.502A pdb=" N VAL R 246 " --> pdb=" O HIS R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 274 Processing helix chain 'R' and resid 275 through 285 removed outlier: 3.628A pdb=" N VAL R 279 " --> pdb=" O HIS R 275 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR R 285 " --> pdb=" O VAL R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 307 Processing helix chain 'R' and resid 308 through 318 Processing helix chain 'S' and resid 24 through 45 removed outlier: 3.593A pdb=" N SER S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE S 40 " --> pdb=" O GLU S 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY S 42 " --> pdb=" O THR S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 72 removed outlier: 3.597A pdb=" N GLU S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP S 62 " --> pdb=" O GLU S 58 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY S 68 " --> pdb=" O TYR S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 98 removed outlier: 4.167A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU S 88 " --> pdb=" O ILE S 84 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS S 89 " --> pdb=" O ALA S 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU S 90 " --> pdb=" O TRP S 86 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 137 removed outlier: 3.625A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR S 120 " --> pdb=" O ASP S 116 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR S 131 " --> pdb=" O ARG S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 165 removed outlier: 3.689A pdb=" N TYR S 145 " --> pdb=" O GLU S 141 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA S 148 " --> pdb=" O ALA S 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP S 151 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE S 154 " --> pdb=" O SER S 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU S 155 " --> pdb=" O ASP S 151 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU S 161 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE S 162 " --> pdb=" O ARG S 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 45 removed outlier: 3.623A pdb=" N SER T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE T 40 " --> pdb=" O GLU T 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY T 42 " --> pdb=" O THR T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.646A pdb=" N GLU T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP T 62 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY T 68 " --> pdb=" O TYR T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 98 removed outlier: 4.129A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU T 88 " --> pdb=" O ILE T 84 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU T 90 " --> pdb=" O TRP T 86 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET T 97 " --> pdb=" O ARG T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 137 removed outlier: 3.631A pdb=" N LEU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR T 120 " --> pdb=" O ASP T 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR T 131 " --> pdb=" O ARG T 127 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG T 134 " --> pdb=" O LEU T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 165 removed outlier: 3.689A pdb=" N TYR T 145 " --> pdb=" O GLU T 141 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA T 148 " --> pdb=" O ALA T 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP T 151 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE T 154 " --> pdb=" O SER T 150 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG T 158 " --> pdb=" O PHE T 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU T 161 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE T 162 " --> pdb=" O ARG T 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 31 removed outlier: 3.742A pdb=" N LEU X 22 " --> pdb=" O PRO X 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU X 23 " --> pdb=" O GLY X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 89 removed outlier: 3.769A pdb=" N ALA X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL X 87 " --> pdb=" O SER X 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22 removed outlier: 6.191A pdb=" N ASN A 149 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS A 166 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU A 119 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASN A 121 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 15 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 123 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU A 17 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU A 125 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A 19 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY A 127 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP A 21 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.470A pdb=" N ALA O 49 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 100 " --> pdb=" O VAL X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.285A pdb=" N ALA N 49 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL X 100 " --> pdb=" O VAL O 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.792A pdb=" N VAL O 100 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA X 49 " --> pdb=" O PHE O 44 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'X' and resid 13 through 14 514 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1626 1.29 - 1.42: 2012 1.42 - 1.55: 5377 1.55 - 1.68: 2 1.68 - 1.81: 50 Bond restraints: 9067 Sorted by residual: bond pdb=" C LEU R 90 " pdb=" N ILE R 91 " ideal model delta sigma weight residual 1.335 1.232 0.102 1.26e-02 6.30e+03 6.61e+01 bond pdb=" C PHE A 223 " pdb=" N VAL A 224 " ideal model delta sigma weight residual 1.331 1.250 0.081 1.24e-02 6.50e+03 4.23e+01 bond pdb=" C LYS A 156 " pdb=" O LYS A 156 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.17e-02 7.31e+03 3.02e+01 bond pdb=" C VAL O 5 " pdb=" N ILE O 6 " ideal model delta sigma weight residual 1.330 1.262 0.068 1.25e-02 6.40e+03 2.95e+01 bond pdb=" C GLU R 81 " pdb=" N GLU R 82 " ideal model delta sigma weight residual 1.335 1.260 0.074 1.38e-02 5.25e+03 2.91e+01 ... (remaining 9062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11398 1.71 - 3.43: 753 3.43 - 5.14: 79 5.14 - 6.86: 11 6.86 - 8.57: 3 Bond angle restraints: 12244 Sorted by residual: angle pdb=" C VAL A 224 " pdb=" N THR A 225 " pdb=" CA THR A 225 " ideal model delta sigma weight residual 122.73 114.16 8.57 1.62e+00 3.81e-01 2.80e+01 angle pdb=" O PHE A 223 " pdb=" C PHE A 223 " pdb=" N VAL A 224 " ideal model delta sigma weight residual 123.23 117.38 5.85 1.30e+00 5.92e-01 2.02e+01 angle pdb=" N ILE A 123 " pdb=" CA ILE A 123 " pdb=" C ILE A 123 " ideal model delta sigma weight residual 108.48 114.29 -5.81 1.44e+00 4.82e-01 1.63e+01 angle pdb=" N ILE R 162 " pdb=" CA ILE R 162 " pdb=" C ILE R 162 " ideal model delta sigma weight residual 110.42 114.18 -3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N VAL A 224 " ideal model delta sigma weight residual 116.01 121.67 -5.66 1.49e+00 4.50e-01 1.45e+01 ... (remaining 12239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5279 17.67 - 35.34: 157 35.34 - 53.02: 36 53.02 - 70.69: 7 70.69 - 88.36: 5 Dihedral angle restraints: 5484 sinusoidal: 2166 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ASP A 180 " pdb=" CB ASP A 180 " pdb=" CG ASP A 180 " pdb=" OD1 ASP A 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.07 58.07 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA PRO A 196 " pdb=" C PRO A 196 " pdb=" N ASP A 197 " pdb=" CA ASP A 197 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N THR A 97 " pdb=" CA THR A 97 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 966 0.044 - 0.088: 367 0.088 - 0.133: 89 0.133 - 0.177: 8 0.177 - 0.221: 4 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA GLU A 5 " pdb=" N GLU A 5 " pdb=" C GLU A 5 " pdb=" CB GLU A 5 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LYS A 41 " pdb=" N LYS A 41 " pdb=" C LYS A 41 " pdb=" CB LYS A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LYS A 156 " pdb=" N LYS A 156 " pdb=" C LYS A 156 " pdb=" CB LYS A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1431 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO A 66 " -0.040 2.00e-02 2.50e+03 3.40e-02 2.90e+01 pdb=" CG2 CRO A 66 " 0.068 2.00e-02 2.50e+03 pdb=" C1 CRO A 66 " -0.033 2.00e-02 2.50e+03 pdb=" C2 CRO A 66 " -0.024 2.00e-02 2.50e+03 pdb=" CA1 CRO A 66 " 0.011 2.00e-02 2.50e+03 pdb=" CA2 CRO A 66 " -0.015 2.00e-02 2.50e+03 pdb=" CA3 CRO A 66 " 0.055 2.00e-02 2.50e+03 pdb=" N2 CRO A 66 " -0.017 2.00e-02 2.50e+03 pdb=" N3 CRO A 66 " -0.005 2.00e-02 2.50e+03 pdb=" O2 CRO A 66 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB2 CRO A 66 " 0.014 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG2 CRO A 66 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 CRO A 66 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 CRO A 66 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 CRO A 66 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 CRO A 66 " 0.016 2.00e-02 2.50e+03 pdb=" CZ CRO A 66 " -0.006 2.00e-02 2.50e+03 pdb=" OH CRO A 66 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 162 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.89e+00 pdb=" C ILE R 162 " -0.054 2.00e-02 2.50e+03 pdb=" O ILE R 162 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU R 163 " 0.018 2.00e-02 2.50e+03 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 151 2.68 - 3.23: 8286 3.23 - 3.79: 12619 3.79 - 4.34: 18591 4.34 - 4.90: 30616 Nonbonded interactions: 70263 Sorted by model distance: nonbonded pdb=" NH1 ARG X 77 " pdb=" OE2 GLU X 108 " model vdw 2.125 3.120 nonbonded pdb=" NH1 ARG O 77 " pdb=" OE2 GLU O 108 " model vdw 2.153 3.120 nonbonded pdb=" OD2 ASP T 62 " pdb=" OH TYR T 145 " model vdw 2.206 3.040 nonbonded pdb=" NH1 ARG N 77 " pdb=" OE2 GLU N 108 " model vdw 2.295 3.120 nonbonded pdb=" OD2 ASP R 62 " pdb=" OH TYR R 145 " model vdw 2.316 3.040 ... (remaining 70258 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 'N' selection = chain 'O' selection = chain 'X' } ncs_group { reference = chain 'S' selection = chain 'T' } 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: 1.470 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 : 0.010 0.162 9069 Z= 0.627 Angle : 0.935 8.573 12244 Z= 0.597 Chirality : 0.048 0.221 1434 Planarity : 0.006 0.072 1579 Dihedral : 9.922 88.359 3352 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.21 % Allowed : 1.83 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.20), residues: 1149 helix: -4.05 (0.12), residues: 551 sheet: 0.50 (0.33), residues: 205 loop : -1.02 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 43 TYR 0.012 0.002 TYR A 151 PHE 0.017 0.002 PHE A 165 TRP 0.014 0.002 TRP S 86 HIS 0.008 0.002 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.01030 ( 9067) covalent geometry : angle 0.93470 (12244) hydrogen bonds : bond 0.28611 ( 514) hydrogen bonds : angle 9.35561 ( 1458) Misc. bond : bond 0.11494 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 397 time to evaluate : 0.346 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: N 105 GLU cc_start: 0.7812 (tt0) cc_final: 0.7511 (tt0) REVERT: R 97 MET cc_start: 0.7590 (mtt) cc_final: 0.7274 (mtt) REVERT: R 211 GLU cc_start: 0.8396 (pm20) cc_final: 0.7240 (pm20) REVERT: T 67 MET cc_start: 0.7829 (mtp) cc_final: 0.7590 (mtp) outliers start: 2 outliers final: 0 residues processed: 398 average time/residue: 0.1086 time to fit residues: 57.1362 Evaluate side-chains 272 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN ** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 ASN T 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.171809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.127505 restraints weight = 11751.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131583 restraints weight = 6312.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.134342 restraints weight = 4050.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136159 restraints weight = 2914.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137546 restraints weight = 2285.622| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9069 Z= 0.143 Angle : 0.575 10.582 12244 Z= 0.302 Chirality : 0.041 0.138 1434 Planarity : 0.005 0.046 1579 Dihedral : 4.740 57.633 1254 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.44 % Allowed : 12.67 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1149 helix: -1.57 (0.19), residues: 550 sheet: 1.02 (0.32), residues: 224 loop : -0.24 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 51 TYR 0.016 0.002 TYR A 200 PHE 0.019 0.002 PHE A 165 TRP 0.012 0.002 TRP T 86 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9067) covalent geometry : angle 0.57526 (12244) hydrogen bonds : bond 0.05511 ( 514) hydrogen bonds : angle 5.06564 ( 1458) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.6257 (tttm) cc_final: 0.5764 (tppt) REVERT: A 114 PHE cc_start: 0.5454 (m-80) cc_final: 0.4548 (m-80) REVERT: N 50 TYR cc_start: 0.9011 (p90) cc_final: 0.8689 (p90) REVERT: O 13 ARG cc_start: 0.7558 (mpp80) cc_final: 0.6215 (mtm110) REVERT: O 45 VAL cc_start: 0.8883 (t) cc_final: 0.8583 (m) REVERT: R 35 ASP cc_start: 0.7327 (t0) cc_final: 0.6975 (t0) REVERT: R 262 ILE cc_start: 0.7669 (mm) cc_final: 0.7374 (mt) REVERT: S 53 LYS cc_start: 0.7950 (tttm) cc_final: 0.7728 (ttmt) REVERT: S 119 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8155 (ttp80) REVERT: S 155 LEU cc_start: 0.8216 (mm) cc_final: 0.7936 (mt) outliers start: 32 outliers final: 23 residues processed: 320 average time/residue: 0.1004 time to fit residues: 43.4067 Evaluate side-chains 293 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 252 ASN Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 209 HIS ** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.161526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.117399 restraints weight = 11673.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121215 restraints weight = 6333.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123869 restraints weight = 4126.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125571 restraints weight = 3004.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126902 restraints weight = 2386.835| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9069 Z= 0.285 Angle : 0.682 8.600 12244 Z= 0.356 Chirality : 0.045 0.141 1434 Planarity : 0.005 0.053 1579 Dihedral : 5.012 38.147 1254 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.69 % Allowed : 16.11 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1149 helix: -0.36 (0.20), residues: 547 sheet: 1.27 (0.32), residues: 221 loop : -0.46 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 43 TYR 0.017 0.002 TYR T 47 PHE 0.029 0.003 PHE A 145 TRP 0.019 0.002 TRP T 86 HIS 0.011 0.002 HIS O 3 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 9067) covalent geometry : angle 0.68250 (12244) hydrogen bonds : bond 0.06657 ( 514) hydrogen bonds : angle 5.13017 ( 1458) Misc. bond : bond 0.00112 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7909 (tmm160) REVERT: A 101 LYS cc_start: 0.6160 (tttm) cc_final: 0.5807 (tppt) REVERT: A 126 LYS cc_start: 0.7413 (tptt) cc_final: 0.6803 (pttp) REVERT: A 215 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7798 (mtm180) REVERT: N 23 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7473 (mt-10) REVERT: N 39 ASP cc_start: 0.7698 (m-30) cc_final: 0.7079 (m-30) REVERT: N 50 TYR cc_start: 0.9207 (p90) cc_final: 0.8791 (p90) REVERT: N 117 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7722 (ttp80) REVERT: O 13 ARG cc_start: 0.7896 (mpp80) cc_final: 0.7508 (mtm110) REVERT: O 45 VAL cc_start: 0.9015 (t) cc_final: 0.8784 (m) REVERT: R 111 GLU cc_start: 0.8328 (mp0) cc_final: 0.7829 (mp0) REVERT: R 136 PHE cc_start: 0.8244 (m-80) cc_final: 0.7912 (m-80) REVERT: R 176 GLN cc_start: 0.8412 (mp10) cc_final: 0.7682 (mp10) REVERT: S 65 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7627 (mttm) REVERT: S 110 LEU cc_start: 0.8524 (tp) cc_final: 0.8318 (tp) REVERT: S 111 GLU cc_start: 0.7757 (mp0) cc_final: 0.7405 (mt-10) REVERT: T 95 MET cc_start: 0.8123 (tpp) cc_final: 0.7565 (ttt) REVERT: T 111 GLU cc_start: 0.8336 (mp0) cc_final: 0.8091 (mp0) outliers start: 53 outliers final: 34 residues processed: 292 average time/residue: 0.0908 time to fit residues: 36.7392 Evaluate side-chains 281 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 100 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain X residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 64 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.166566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.122761 restraints weight = 11666.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126804 restraints weight = 6176.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129603 restraints weight = 3941.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.131379 restraints weight = 2823.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132759 restraints weight = 2211.536| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9069 Z= 0.114 Angle : 0.503 7.462 12244 Z= 0.266 Chirality : 0.040 0.127 1434 Planarity : 0.003 0.046 1579 Dihedral : 4.385 29.045 1254 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.01 % Allowed : 19.01 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1149 helix: 0.62 (0.21), residues: 548 sheet: 1.48 (0.32), residues: 222 loop : -0.29 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 77 TYR 0.013 0.001 TYR A 200 PHE 0.019 0.001 PHE A 165 TRP 0.012 0.001 TRP R 86 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9067) covalent geometry : angle 0.50280 (12244) hydrogen bonds : bond 0.04358 ( 514) hydrogen bonds : angle 4.44224 ( 1458) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.6174 (tttm) cc_final: 0.5844 (tppt) REVERT: A 126 LYS cc_start: 0.7447 (tptt) cc_final: 0.6819 (pttp) REVERT: A 194 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6350 (tt) REVERT: A 215 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7583 (mtm180) REVERT: N 23 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7498 (mt-10) REVERT: N 50 TYR cc_start: 0.9163 (p90) cc_final: 0.8791 (p90) REVERT: O 13 ARG cc_start: 0.7764 (mpp80) cc_final: 0.7524 (mtm110) REVERT: O 15 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7066 (mm-30) REVERT: O 45 VAL cc_start: 0.9011 (t) cc_final: 0.8777 (m) REVERT: R 35 ASP cc_start: 0.7355 (t0) cc_final: 0.6811 (t0) REVERT: R 176 GLN cc_start: 0.8438 (mp10) cc_final: 0.7752 (mp10) REVERT: R 194 ASP cc_start: 0.8045 (t0) cc_final: 0.7807 (t0) REVERT: R 210 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7221 (mt) REVERT: S 65 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7621 (mttm) REVERT: T 52 MET cc_start: 0.8056 (mmm) cc_final: 0.7820 (mmm) outliers start: 28 outliers final: 20 residues processed: 273 average time/residue: 0.0928 time to fit residues: 34.9570 Evaluate side-chains 262 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 ASN R 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.165349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122085 restraints weight = 11593.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126076 restraints weight = 6093.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128865 restraints weight = 3881.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130661 restraints weight = 2779.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.131699 restraints weight = 2176.826| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9069 Z= 0.125 Angle : 0.506 6.804 12244 Z= 0.266 Chirality : 0.040 0.135 1434 Planarity : 0.003 0.040 1579 Dihedral : 4.213 30.335 1254 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.97 % Allowed : 19.55 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1149 helix: 1.09 (0.21), residues: 548 sheet: 1.58 (0.32), residues: 222 loop : -0.32 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 30 TYR 0.017 0.001 TYR X 61 PHE 0.020 0.001 PHE A 165 TRP 0.010 0.002 TRP R 86 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9067) covalent geometry : angle 0.50583 (12244) hydrogen bonds : bond 0.04183 ( 514) hydrogen bonds : angle 4.29498 ( 1458) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8210 (tppt) cc_final: 0.7972 (tppt) REVERT: A 80 ARG cc_start: 0.7923 (tmt170) cc_final: 0.7671 (tmt170) REVERT: A 101 LYS cc_start: 0.6032 (tttm) cc_final: 0.5730 (tppt) REVERT: A 126 LYS cc_start: 0.7406 (tptt) cc_final: 0.6830 (pttt) REVERT: A 194 LEU cc_start: 0.6942 (mt) cc_final: 0.6649 (tt) REVERT: A 215 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7557 (mtm180) REVERT: N 50 TYR cc_start: 0.9196 (p90) cc_final: 0.8808 (p90) REVERT: O 15 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7158 (mm-30) REVERT: O 98 GLU cc_start: 0.8413 (tp30) cc_final: 0.8204 (tp30) REVERT: R 35 ASP cc_start: 0.7397 (t0) cc_final: 0.6793 (t0) REVERT: R 43 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8461 (tm-30) REVERT: R 111 GLU cc_start: 0.8272 (mp0) cc_final: 0.7726 (mp0) REVERT: R 176 GLN cc_start: 0.8368 (mp10) cc_final: 0.7700 (mp10) REVERT: R 210 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7243 (mt) REVERT: R 261 ASN cc_start: 0.8278 (m-40) cc_final: 0.8059 (m-40) REVERT: S 65 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7615 (mttm) REVERT: S 135 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6382 (tm-30) REVERT: T 52 MET cc_start: 0.8114 (mmm) cc_final: 0.7864 (mpp) outliers start: 37 outliers final: 26 residues processed: 267 average time/residue: 0.0979 time to fit residues: 35.7392 Evaluate side-chains 269 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 252 ASN Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain X residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.157159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114257 restraints weight = 11843.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118024 restraints weight = 6340.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.120603 restraints weight = 4092.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.122237 restraints weight = 2974.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.123532 restraints weight = 2358.545| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 9069 Z= 0.318 Angle : 0.706 7.834 12244 Z= 0.366 Chirality : 0.046 0.147 1434 Planarity : 0.005 0.041 1579 Dihedral : 5.233 54.820 1254 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.44 % Allowed : 18.80 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1149 helix: 0.46 (0.21), residues: 548 sheet: 1.69 (0.32), residues: 214 loop : -0.74 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG T 124 TYR 0.017 0.002 TYR X 61 PHE 0.020 0.002 PHE A 165 TRP 0.016 0.002 TRP T 86 HIS 0.010 0.002 HIS O 3 Details of bonding type rmsd covalent geometry : bond 0.00773 ( 9067) covalent geometry : angle 0.70616 (12244) hydrogen bonds : bond 0.06504 ( 514) hydrogen bonds : angle 5.08858 ( 1458) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.6106 (tttm) cc_final: 0.5803 (tppt) REVERT: A 126 LYS cc_start: 0.7404 (tptt) cc_final: 0.6809 (pttt) REVERT: A 131 LYS cc_start: 0.7943 (mttt) cc_final: 0.7460 (mmtm) REVERT: O 98 GLU cc_start: 0.8549 (tp30) cc_final: 0.8335 (tp30) REVERT: R 35 ASP cc_start: 0.7479 (t0) cc_final: 0.7084 (t0) REVERT: R 43 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8594 (tm-30) REVERT: R 173 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8435 (ttp80) REVERT: R 176 GLN cc_start: 0.8311 (mp10) cc_final: 0.7586 (mp10) REVERT: R 210 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7286 (mt) REVERT: R 242 HIS cc_start: 0.8477 (m-70) cc_final: 0.8276 (m90) REVERT: S 36 GLU cc_start: 0.7867 (tt0) cc_final: 0.7654 (tt0) REVERT: S 65 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7747 (mttm) REVERT: S 111 GLU cc_start: 0.7738 (mp0) cc_final: 0.7487 (mt-10) REVERT: S 135 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6645 (tm-30) REVERT: T 81 GLU cc_start: 0.7567 (pm20) cc_final: 0.7243 (pm20) REVERT: T 95 MET cc_start: 0.8109 (tpp) cc_final: 0.7538 (ttt) outliers start: 60 outliers final: 44 residues processed: 263 average time/residue: 0.0986 time to fit residues: 34.8083 Evaluate side-chains 277 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain O residue 97 GLU Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 100 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 155 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 252 ASN R 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.163889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.120386 restraints weight = 11720.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.124325 restraints weight = 6161.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127042 restraints weight = 3939.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.128909 restraints weight = 2845.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130230 restraints weight = 2232.693| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9069 Z= 0.121 Angle : 0.527 8.766 12244 Z= 0.275 Chirality : 0.040 0.143 1434 Planarity : 0.003 0.042 1579 Dihedral : 4.637 50.516 1254 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.40 % Allowed : 20.73 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1149 helix: 1.29 (0.21), residues: 548 sheet: 1.82 (0.33), residues: 215 loop : -0.51 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 158 TYR 0.015 0.001 TYR X 61 PHE 0.020 0.001 PHE A 165 TRP 0.015 0.002 TRP R 86 HIS 0.006 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9067) covalent geometry : angle 0.52659 (12244) hydrogen bonds : bond 0.04189 ( 514) hydrogen bonds : angle 4.32961 ( 1458) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7466 (mmm) cc_final: 0.7049 (mmt) REVERT: A 80 ARG cc_start: 0.7967 (tmt170) cc_final: 0.7691 (tpt90) REVERT: A 88 MET cc_start: 0.6586 (mmm) cc_final: 0.6174 (mmm) REVERT: A 101 LYS cc_start: 0.6035 (tttm) cc_final: 0.5781 (tppt) REVERT: A 126 LYS cc_start: 0.7392 (tptt) cc_final: 0.6641 (pttp) REVERT: A 131 LYS cc_start: 0.7912 (mttt) cc_final: 0.7289 (mmtm) REVERT: A 194 LEU cc_start: 0.7246 (mt) cc_final: 0.6869 (tt) REVERT: A 215 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7554 (mtm180) REVERT: N 50 TYR cc_start: 0.9095 (p90) cc_final: 0.8756 (p90) REVERT: O 98 GLU cc_start: 0.8559 (tp30) cc_final: 0.8329 (tp30) REVERT: R 35 ASP cc_start: 0.7332 (t0) cc_final: 0.6875 (t0) REVERT: R 111 GLU cc_start: 0.8308 (mp0) cc_final: 0.7759 (mp0) REVERT: R 176 GLN cc_start: 0.8209 (mp10) cc_final: 0.7547 (mp10) REVERT: R 210 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6953 (mt) REVERT: S 65 LYS cc_start: 0.7868 (mmtp) cc_final: 0.7635 (mttm) REVERT: S 119 ARG cc_start: 0.8438 (ttp80) cc_final: 0.7946 (ttt-90) REVERT: S 135 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6477 (tm-30) REVERT: T 52 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7722 (mmm) REVERT: T 58 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6532 (mm-30) outliers start: 41 outliers final: 30 residues processed: 262 average time/residue: 0.0924 time to fit residues: 33.2888 Evaluate side-chains 273 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.162500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119471 restraints weight = 11610.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.123370 restraints weight = 6097.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.126075 restraints weight = 3910.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127898 restraints weight = 2821.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129164 restraints weight = 2212.185| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9069 Z= 0.175 Angle : 0.563 7.649 12244 Z= 0.294 Chirality : 0.042 0.166 1434 Planarity : 0.003 0.040 1579 Dihedral : 4.767 56.696 1254 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.30 % Allowed : 20.62 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1149 helix: 1.32 (0.21), residues: 548 sheet: 1.87 (0.33), residues: 213 loop : -0.60 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 30 TYR 0.015 0.001 TYR X 61 PHE 0.019 0.002 PHE A 165 TRP 0.011 0.002 TRP R 229 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9067) covalent geometry : angle 0.56305 (12244) hydrogen bonds : bond 0.04792 ( 514) hydrogen bonds : angle 4.50220 ( 1458) Misc. bond : bond 0.00094 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7439 (mmm) cc_final: 0.7010 (mmm) REVERT: A 80 ARG cc_start: 0.7925 (tmt170) cc_final: 0.7669 (tpt90) REVERT: A 88 MET cc_start: 0.6712 (mmm) cc_final: 0.6167 (mmm) REVERT: A 101 LYS cc_start: 0.5987 (tttm) cc_final: 0.5745 (tppt) REVERT: A 126 LYS cc_start: 0.7389 (tptt) cc_final: 0.6706 (pttp) REVERT: A 131 LYS cc_start: 0.7882 (mttt) cc_final: 0.7335 (mmtm) REVERT: A 194 LEU cc_start: 0.7411 (mt) cc_final: 0.6985 (tt) REVERT: A 215 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7344 (mtm180) REVERT: N 50 TYR cc_start: 0.9144 (p90) cc_final: 0.8812 (p90) REVERT: R 35 ASP cc_start: 0.7459 (t0) cc_final: 0.6976 (t0) REVERT: R 111 GLU cc_start: 0.8381 (mp0) cc_final: 0.7844 (mp0) REVERT: R 176 GLN cc_start: 0.8129 (mp10) cc_final: 0.7467 (mp10) REVERT: S 65 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7646 (mttm) REVERT: S 135 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6519 (tm-30) REVERT: T 52 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: T 95 MET cc_start: 0.8024 (tpp) cc_final: 0.7482 (ttt) REVERT: X 27 LYS cc_start: 0.7971 (tppp) cc_final: 0.7691 (tppt) outliers start: 40 outliers final: 33 residues processed: 267 average time/residue: 0.1016 time to fit residues: 36.8078 Evaluate side-chains 272 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.165798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122709 restraints weight = 11602.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126688 restraints weight = 6061.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129423 restraints weight = 3869.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.131330 restraints weight = 2784.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132586 restraints weight = 2166.720| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9069 Z= 0.123 Angle : 0.538 8.703 12244 Z= 0.279 Chirality : 0.040 0.138 1434 Planarity : 0.003 0.043 1579 Dihedral : 4.517 52.936 1254 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.87 % Allowed : 21.27 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1149 helix: 1.70 (0.21), residues: 550 sheet: 1.85 (0.33), residues: 215 loop : -0.56 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 30 TYR 0.015 0.001 TYR X 61 PHE 0.019 0.001 PHE A 165 TRP 0.013 0.002 TRP R 86 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9067) covalent geometry : angle 0.53762 (12244) hydrogen bonds : bond 0.04039 ( 514) hydrogen bonds : angle 4.25435 ( 1458) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7355 (mmm) cc_final: 0.6943 (mmt) REVERT: A 80 ARG cc_start: 0.7942 (tmt170) cc_final: 0.7646 (tpt90) REVERT: A 88 MET cc_start: 0.6745 (mmm) cc_final: 0.6242 (mmm) REVERT: A 101 LYS cc_start: 0.5893 (tttm) cc_final: 0.5619 (tppt) REVERT: A 126 LYS cc_start: 0.7390 (tptt) cc_final: 0.6647 (pttp) REVERT: A 131 LYS cc_start: 0.7873 (mttt) cc_final: 0.7292 (mmtm) REVERT: A 194 LEU cc_start: 0.7449 (mt) cc_final: 0.7005 (tt) REVERT: A 215 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7409 (mtm180) REVERT: N 50 TYR cc_start: 0.9095 (p90) cc_final: 0.8805 (p90) REVERT: R 35 ASP cc_start: 0.7461 (t0) cc_final: 0.6976 (t0) REVERT: R 82 GLU cc_start: 0.7592 (tp30) cc_final: 0.7391 (tp30) REVERT: R 111 GLU cc_start: 0.8318 (mp0) cc_final: 0.7771 (mp0) REVERT: R 176 GLN cc_start: 0.8143 (mp10) cc_final: 0.7466 (mp10) REVERT: R 277 GLU cc_start: 0.7972 (tt0) cc_final: 0.7147 (mp0) REVERT: S 65 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7588 (mttm) REVERT: S 119 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7921 (ttp80) REVERT: T 52 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7759 (mmm) REVERT: X 27 LYS cc_start: 0.7938 (tppp) cc_final: 0.7670 (tppt) outliers start: 36 outliers final: 29 residues processed: 268 average time/residue: 0.1010 time to fit residues: 36.5260 Evaluate side-chains 278 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.0000 chunk 87 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.172774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131460 restraints weight = 11513.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135453 restraints weight = 5977.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138201 restraints weight = 3783.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140022 restraints weight = 2705.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.141367 restraints weight = 2114.884| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9069 Z= 0.105 Angle : 0.515 8.026 12244 Z= 0.267 Chirality : 0.040 0.147 1434 Planarity : 0.003 0.044 1579 Dihedral : 4.232 46.831 1254 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.22 % Allowed : 21.59 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1149 helix: 2.04 (0.21), residues: 551 sheet: 1.94 (0.33), residues: 215 loop : -0.51 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 51 TYR 0.014 0.001 TYR X 61 PHE 0.019 0.001 PHE A 165 TRP 0.016 0.002 TRP A 57 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9067) covalent geometry : angle 0.51452 (12244) hydrogen bonds : bond 0.03493 ( 514) hydrogen bonds : angle 4.09949 ( 1458) Misc. bond : bond 0.00055 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7845 (tmt170) cc_final: 0.7641 (tmt170) REVERT: A 88 MET cc_start: 0.6875 (mmm) cc_final: 0.6359 (mmm) REVERT: A 101 LYS cc_start: 0.5831 (tttm) cc_final: 0.5563 (tppt) REVERT: A 126 LYS cc_start: 0.7404 (tptt) cc_final: 0.6669 (pttt) REVERT: A 131 LYS cc_start: 0.7922 (mttt) cc_final: 0.7299 (mmtm) REVERT: A 194 LEU cc_start: 0.7536 (mt) cc_final: 0.7314 (tt) REVERT: A 215 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7290 (mtm180) REVERT: N 50 TYR cc_start: 0.9028 (p90) cc_final: 0.8727 (p90) REVERT: R 35 ASP cc_start: 0.7312 (t0) cc_final: 0.6818 (t0) REVERT: R 82 GLU cc_start: 0.7659 (tp30) cc_final: 0.7454 (tp30) REVERT: R 176 GLN cc_start: 0.8050 (mp10) cc_final: 0.7470 (mp10) REVERT: R 277 GLU cc_start: 0.7962 (tt0) cc_final: 0.7220 (mp0) REVERT: R 294 LYS cc_start: 0.7887 (mptt) cc_final: 0.7665 (mptt) REVERT: R 295 PHE cc_start: 0.7687 (m-80) cc_final: 0.7448 (m-80) REVERT: S 58 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7720 (mt-10) REVERT: S 65 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7536 (mttm) REVERT: S 119 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7908 (ttp80) REVERT: T 52 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: X 27 LYS cc_start: 0.7906 (tppp) cc_final: 0.7642 (tppt) outliers start: 30 outliers final: 24 residues processed: 266 average time/residue: 0.0960 time to fit residues: 34.8806 Evaluate side-chains 266 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.168135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126264 restraints weight = 11403.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130066 restraints weight = 6004.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132806 restraints weight = 3854.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.134639 restraints weight = 2777.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135964 restraints weight = 2168.608| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9069 Z= 0.140 Angle : 0.554 8.506 12244 Z= 0.288 Chirality : 0.041 0.164 1434 Planarity : 0.003 0.043 1579 Dihedral : 4.389 50.886 1254 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.22 % Allowed : 22.23 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.24), residues: 1149 helix: 1.94 (0.21), residues: 552 sheet: 1.82 (0.32), residues: 221 loop : -0.58 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 77 TYR 0.018 0.001 TYR O 114 PHE 0.019 0.001 PHE A 165 TRP 0.021 0.002 TRP A 57 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9067) covalent geometry : angle 0.55436 (12244) hydrogen bonds : bond 0.04081 ( 514) hydrogen bonds : angle 4.21475 ( 1458) Misc. bond : bond 0.00073 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1732.95 seconds wall clock time: 30 minutes 25.97 seconds (1825.97 seconds total)