Starting phenix.real_space_refine on Fri Sep 11 10:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nhv_9374/09_2026/6nhv_9374.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nhv_9374/09_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_9374/09_2026/6nhv_9374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nhv_9374/09_2026/6nhv_9374.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nhv_9374/09_2026/6nhv_9374.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nhv_9374/09_2026/6nhv_9374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nhv_9374/09_2026/6nhv_9374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nhv_9374/09_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-2.2.1-6174/lib/python3.11/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: 2.03, per 1000 atoms: 0.23 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: 0.78 Conformation dependent library (CDL) restraints added in 355.7 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: 0.25 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: 1.40 Time building geometry restraints manager: 1.00 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.220 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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/Z covalent geometry : bond 0.01030 / 0.60 ( 9067) covalent geometry : angle 0.93470 / 0.60 (12244) hydrogen bonds : bond 0.28611 / 19.17 ( 514) hydrogen bonds : angle 9.35561 / 6.60 ( 1458) Misc. bond : bond 0.11494 / 6.04 ( 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 : 0.335 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: 0.7273 (mtt) REVERT: R 211 GLU cc_start: 0.8396 (pm20) cc_final: 0.7239 (pm20) REVERT: T 67 MET cc_start: 0.7829 (mtp) cc_final: 0.7591 (mtp) outliers start: 2 outliers final: 0 residues processed: 398 average time/residue: 0.1066 time to fit residues: 56.7213 Evaluate side-chains 271 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3848 r_free = 0.3848 target = 0.172389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128413 restraints weight = 11774.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132422 restraints weight = 6281.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.135170 restraints weight = 4035.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.137071 restraints weight = 2903.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.138316 restraints weight = 2266.458| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9069 Z= 0.142 Angle : 0.573 10.581 12244 Z= 0.301 Chirality : 0.041 0.137 1434 Planarity : 0.005 0.046 1579 Dihedral : 4.725 56.691 1254 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.44 % Allowed : 12.78 % Favored : 83.78 % 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: -1.09 (0.22), residues: 1149 helix: -1.49 (0.19), residues: 546 sheet: 1.03 (0.32), residues: 224 loop : -0.28 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 51 TYR 0.017 0.002 TYR A 200 PHE 0.017 0.002 PHE A 165 TRP 0.012 0.001 TRP R 86 HIS 0.005 0.001 HIS R 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9067) covalent geometry : angle 0.57286 / 0.30 (12244) hydrogen bonds : bond 0.05760 / 3.94 ( 514) hydrogen bonds : angle 5.12411 / 3.53 ( 1458) Misc. bond : bond 0.00060 / 0.03 ( 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 329 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7147 (mtt) cc_final: 0.6892 (mmm) REVERT: A 101 LYS cc_start: 0.6263 (tttm) cc_final: 0.5768 (tppt) REVERT: A 114 PHE cc_start: 0.5111 (m-80) cc_final: 0.4260 (m-80) REVERT: N 50 TYR cc_start: 0.9030 (p90) cc_final: 0.8678 (p90) REVERT: O 13 ARG cc_start: 0.7500 (mpp80) cc_final: 0.6103 (mtm110) REVERT: O 45 VAL cc_start: 0.8845 (t) cc_final: 0.8540 (m) REVERT: R 35 ASP cc_start: 0.7469 (t0) cc_final: 0.7186 (t0) REVERT: R 111 GLU cc_start: 0.8065 (mp0) cc_final: 0.7493 (pm20) REVERT: R 262 ILE cc_start: 0.7678 (mm) cc_final: 0.7364 (mt) REVERT: S 119 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8154 (ttp80) REVERT: S 155 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7914 (mt) outliers start: 32 outliers final: 22 residues processed: 317 average time/residue: 0.0955 time to fit residues: 41.2989 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 : 0.292 ------------------------------------------------------------------------------- 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 S residue 155 LEU 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 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: 1.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 209 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.164015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119699 restraints weight = 11648.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123615 restraints weight = 6290.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126270 restraints weight = 4075.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.128077 restraints weight = 2972.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129289 restraints weight = 2344.028| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9069 Z= 0.223 Angle : 0.606 8.671 12244 Z= 0.318 Chirality : 0.043 0.171 1434 Planarity : 0.004 0.043 1579 Dihedral : 4.706 43.672 1254 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.40 % Allowed : 16.54 % Favored : 79.05 % 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: -0.02 (0.23), residues: 1149 helix: -0.21 (0.21), residues: 547 sheet: 1.33 (0.31), residues: 221 loop : -0.30 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 77 TYR 0.013 0.002 TYR X 61 PHE 0.025 0.003 PHE A 145 TRP 0.016 0.002 TRP T 86 HIS 0.008 0.002 HIS O 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 ( 9067) covalent geometry : angle 0.60595 / 0.32 (12244) hydrogen bonds : bond 0.05890 / 4.05 ( 514) hydrogen bonds : angle 4.91233 / 3.40 ( 1458) Misc. bond : bond 0.00088 / 0.05 ( 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 302 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7955 (tmm160) REVERT: A 101 LYS cc_start: 0.6199 (tttm) cc_final: 0.5821 (tppt) REVERT: A 215 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7794 (mtm180) REVERT: N 50 TYR cc_start: 0.9189 (p90) cc_final: 0.8749 (p90) REVERT: O 13 ARG cc_start: 0.7752 (mpp80) cc_final: 0.7473 (mtm110) REVERT: O 45 VAL cc_start: 0.8957 (t) cc_final: 0.8711 (m) REVERT: O 108 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7593 (mt-10) REVERT: R 35 ASP cc_start: 0.7338 (t0) cc_final: 0.6733 (t0) REVERT: R 111 GLU cc_start: 0.8223 (mp0) cc_final: 0.7644 (pm20) REVERT: R 176 GLN cc_start: 0.8622 (mp10) cc_final: 0.7924 (mp10) REVERT: R 189 ASP cc_start: 0.7927 (t0) cc_final: 0.7710 (t0) REVERT: R 310 ASP cc_start: 0.7088 (t0) cc_final: 0.6556 (p0) REVERT: S 65 LYS cc_start: 0.7753 (mmtp) cc_final: 0.7495 (mttm) REVERT: S 110 LEU cc_start: 0.8434 (tp) cc_final: 0.8168 (tp) REVERT: S 155 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8177 (mt) REVERT: X 23 GLU cc_start: 0.7676 (tt0) cc_final: 0.7407 (tt0) outliers start: 41 outliers final: 26 residues processed: 284 average time/residue: 0.0899 time to fit residues: 35.3224 Evaluate side-chains 267 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 28 ILE 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 228 LEU Chi-restraints excluded: chain R residue 232 THR 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 S residue 131 THR Chi-restraints excluded: chain S residue 155 LEU 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 131 THR Chi-restraints excluded: chain T residue 147 LEU 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: 0.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122925 restraints weight = 11700.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.126781 restraints weight = 6393.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129464 restraints weight = 4174.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131279 restraints weight = 3043.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.132509 restraints weight = 2403.315| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9069 Z= 0.123 Angle : 0.509 7.234 12244 Z= 0.267 Chirality : 0.040 0.121 1434 Planarity : 0.003 0.039 1579 Dihedral : 4.286 31.877 1254 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.08 % Allowed : 18.05 % Favored : 77.87 % 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: 0.74 (0.23), residues: 1149 helix: 0.66 (0.21), residues: 548 sheet: 1.55 (0.32), residues: 222 loop : -0.27 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 77 TYR 0.012 0.001 TYR A 200 PHE 0.020 0.001 PHE A 165 TRP 0.011 0.002 TRP R 86 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9067) covalent geometry : angle 0.50948 / 0.27 (12244) hydrogen bonds : bond 0.04410 / 3.04 ( 514) hydrogen bonds : angle 4.46820 / 3.09 ( 1458) Misc. bond : bond 0.00054 / 0.03 ( 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 291 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.338 Fit side-chains REVERT: A 101 LYS cc_start: 0.6146 (tttm) cc_final: 0.5790 (tppt) REVERT: A 126 LYS cc_start: 0.7462 (tptt) cc_final: 0.7204 (tptt) REVERT: A 194 LEU cc_start: 0.6210 (mt) cc_final: 0.5881 (tt) REVERT: A 215 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7832 (mtm180) REVERT: N 15 GLU cc_start: 0.7918 (tp30) cc_final: 0.7528 (tm-30) REVERT: N 23 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7925 (mt-10) REVERT: N 50 TYR cc_start: 0.9175 (p90) cc_final: 0.8768 (p90) REVERT: O 15 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7134 (mm-30) REVERT: O 45 VAL cc_start: 0.8975 (t) cc_final: 0.8718 (m) REVERT: R 35 ASP cc_start: 0.7346 (t0) cc_final: 0.6717 (t0) REVERT: S 53 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7815 (ttmm) REVERT: S 65 LYS cc_start: 0.7813 (mmtp) cc_final: 0.7586 (mttm) REVERT: S 135 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6404 (tm-30) REVERT: X 23 GLU cc_start: 0.7374 (tt0) cc_final: 0.7173 (tt0) outliers start: 38 outliers final: 26 residues processed: 270 average time/residue: 0.0891 time to fit residues: 33.6141 Evaluate side-chains 266 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 123 ILE 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 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 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 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 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 T residue 156 LEU Chi-restraints excluded: chain X residue 113 SER 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: 1.9990 chunk 12 optimal weight: 0.0020 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.168997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125208 restraints weight = 11615.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.129277 restraints weight = 6098.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132103 restraints weight = 3892.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134011 restraints weight = 2799.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.135356 restraints weight = 2192.329| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9069 Z= 0.101 Angle : 0.487 8.489 12244 Z= 0.256 Chirality : 0.039 0.119 1434 Planarity : 0.003 0.039 1579 Dihedral : 3.980 23.536 1254 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.33 % Allowed : 19.23 % Favored : 77.44 % 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: 1.29 (0.24), residues: 1149 helix: 1.32 (0.21), residues: 550 sheet: 1.63 (0.32), residues: 222 loop : -0.23 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 77 TYR 0.017 0.001 TYR X 61 PHE 0.020 0.001 PHE A 165 TRP 0.011 0.001 TRP R 86 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 9067) covalent geometry : angle 0.48705 / 0.26 (12244) hydrogen bonds : bond 0.03677 / 2.54 ( 514) hydrogen bonds : angle 4.17277 / 2.90 ( 1458) Misc. bond : bond 0.00036 / 0.02 ( 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 293 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8154 (tppt) cc_final: 0.7890 (tppt) REVERT: A 55 VAL cc_start: 0.7615 (m) cc_final: 0.7357 (p) REVERT: A 80 ARG cc_start: 0.7974 (tmt170) cc_final: 0.7191 (tmm160) REVERT: A 101 LYS cc_start: 0.6099 (tttm) cc_final: 0.5819 (tppt) REVERT: A 131 LYS cc_start: 0.7527 (mttt) cc_final: 0.7116 (mmtt) REVERT: A 194 LEU cc_start: 0.6585 (mt) cc_final: 0.5994 (tt) REVERT: N 15 GLU cc_start: 0.7819 (tp30) cc_final: 0.7563 (tm-30) REVERT: N 50 TYR cc_start: 0.9143 (p90) cc_final: 0.8762 (p90) REVERT: O 51 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7253 (ttt-90) REVERT: R 35 ASP cc_start: 0.7367 (t0) cc_final: 0.6746 (t0) REVERT: R 43 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8353 (tm-30) REVERT: R 111 GLU cc_start: 0.8035 (mp0) cc_final: 0.7543 (mp0) REVERT: R 189 ASP cc_start: 0.7992 (t0) cc_final: 0.7763 (t0) REVERT: R 194 ASP cc_start: 0.8072 (t0) cc_final: 0.7811 (t0) REVERT: R 210 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7241 (mt) REVERT: S 53 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7675 (ttmm) REVERT: S 65 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7557 (mttm) REVERT: S 110 LEU cc_start: 0.7749 (tp) cc_final: 0.7508 (tp) REVERT: S 119 ARG cc_start: 0.8404 (ttp80) cc_final: 0.7996 (ttp80) outliers start: 31 outliers final: 22 residues processed: 273 average time/residue: 0.0889 time to fit residues: 33.6279 Evaluate side-chains 268 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 62 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 N residue 32 SER Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 59 ARG 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 R residue 234 LEU Chi-restraints excluded: chain R residue 252 ASN Chi-restraints excluded: chain S residue 104 VAL 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 T residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.159866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.117194 restraints weight = 11774.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.120972 restraints weight = 6273.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.123543 restraints weight = 4022.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125279 restraints weight = 2910.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.126581 restraints weight = 2281.989| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9069 Z= 0.235 Angle : 0.616 7.049 12244 Z= 0.320 Chirality : 0.043 0.133 1434 Planarity : 0.004 0.039 1579 Dihedral : 4.545 37.210 1254 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.48 % Allowed : 18.26 % Favored : 76.26 % 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: 0.91 (0.23), residues: 1149 helix: 1.02 (0.21), residues: 546 sheet: 1.60 (0.32), residues: 221 loop : -0.53 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 30 TYR 0.015 0.002 TYR X 61 PHE 0.018 0.002 PHE A 165 TRP 0.013 0.002 TRP T 86 HIS 0.007 0.001 HIS O 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 ( 9067) covalent geometry : angle 0.61592 / 0.32 (12244) hydrogen bonds : bond 0.05548 / 3.83 ( 514) hydrogen bonds : angle 4.74449 / 3.29 ( 1458) Misc. bond : bond 0.00104 / 0.05 ( 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 303 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.6032 (tttm) cc_final: 0.5761 (tppt) REVERT: A 215 ARG cc_start: 0.7639 (mtm180) cc_final: 0.6931 (ptm160) REVERT: N 50 TYR cc_start: 0.9222 (p90) cc_final: 0.8866 (p90) REVERT: R 35 ASP cc_start: 0.7447 (t0) cc_final: 0.7047 (t0) REVERT: R 111 GLU cc_start: 0.8331 (mp0) cc_final: 0.7775 (mp0) REVERT: R 176 GLN cc_start: 0.7894 (mp10) cc_final: 0.7235 (mp10) REVERT: R 210 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7282 (mt) REVERT: S 36 GLU cc_start: 0.7819 (tt0) cc_final: 0.7592 (tt0) REVERT: S 65 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7657 (mttm) REVERT: S 110 LEU cc_start: 0.8518 (tp) cc_final: 0.8261 (tp) REVERT: S 135 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6509 (tm-30) REVERT: T 52 MET cc_start: 0.8140 (mmm) cc_final: 0.7573 (mmt) REVERT: T 81 GLU cc_start: 0.7496 (pm20) cc_final: 0.7229 (pm20) REVERT: T 95 MET cc_start: 0.7957 (tpp) cc_final: 0.7333 (ttt) outliers start: 51 outliers final: 36 residues processed: 275 average time/residue: 0.0873 time to fit residues: 33.5584 Evaluate side-chains 268 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 62 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 153 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 ASP 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 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 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 92 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 T residue 156 LEU Chi-restraints excluded: chain X residue 74 ILE 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: 1.9990 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.164290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120576 restraints weight = 11709.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124500 restraints weight = 6172.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127259 restraints weight = 3949.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.129070 restraints weight = 2840.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.130263 restraints weight = 2236.833| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9069 Z= 0.132 Angle : 0.546 8.410 12244 Z= 0.282 Chirality : 0.041 0.162 1434 Planarity : 0.003 0.040 1579 Dihedral : 4.346 38.326 1254 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.08 % Allowed : 19.87 % Favored : 76.05 % 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: 1.34 (0.24), residues: 1149 helix: 1.55 (0.22), residues: 546 sheet: 1.62 (0.32), residues: 222 loop : -0.49 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.016 0.001 TYR X 61 PHE 0.019 0.001 PHE A 165 TRP 0.012 0.002 TRP R 86 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9067) covalent geometry : angle 0.54554 / 0.28 (12244) hydrogen bonds : bond 0.04330 / 3.01 ( 514) hydrogen bonds : angle 4.36471 / 3.04 ( 1458) Misc. bond : bond 0.00087 / 0.04 ( 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: 38 poor density : 245 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7428 (mmm) cc_final: 0.6991 (mmm) REVERT: A 101 LYS cc_start: 0.6011 (tttm) cc_final: 0.5732 (tppt) REVERT: A 131 LYS cc_start: 0.7741 (mttt) cc_final: 0.7273 (mmtm) REVERT: A 194 LEU cc_start: 0.7142 (mt) cc_final: 0.6850 (tt) REVERT: A 215 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7484 (mtm180) REVERT: N 50 TYR cc_start: 0.9194 (p90) cc_final: 0.8836 (p90) REVERT: R 35 ASP cc_start: 0.7472 (t0) cc_final: 0.6975 (t0) REVERT: R 111 GLU cc_start: 0.8213 (mp0) cc_final: 0.7753 (mp0) REVERT: R 176 GLN cc_start: 0.8008 (mp10) cc_final: 0.7386 (mp10) REVERT: R 210 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7351 (mt) REVERT: S 65 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7652 (mttm) REVERT: S 119 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7933 (ttt-90) REVERT: S 135 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6450 (tm-30) REVERT: T 52 MET cc_start: 0.8063 (mmm) cc_final: 0.7624 (mmm) REVERT: T 95 MET cc_start: 0.7929 (tpp) cc_final: 0.7281 (ttt) outliers start: 38 outliers final: 28 residues processed: 260 average time/residue: 0.0914 time to fit residues: 32.6819 Evaluate side-chains 268 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 62 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 A residue 216 ASP 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 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 234 LEU 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 100 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 T residue 156 LEU Chi-restraints excluded: chain X residue 74 ILE 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: 3.9990 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.163626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120962 restraints weight = 11578.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124841 restraints weight = 6146.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127564 restraints weight = 3927.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129353 restraints weight = 2813.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130626 restraints weight = 2206.145| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9069 Z= 0.138 Angle : 0.545 9.195 12244 Z= 0.283 Chirality : 0.041 0.174 1434 Planarity : 0.003 0.041 1579 Dihedral : 4.339 42.110 1254 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.87 % Allowed : 19.76 % Favored : 76.37 % 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: 1.48 (0.24), residues: 1149 helix: 1.72 (0.22), residues: 546 sheet: 1.62 (0.32), residues: 222 loop : -0.46 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 30 TYR 0.014 0.001 TYR X 61 PHE 0.019 0.001 PHE A 165 TRP 0.012 0.002 TRP R 229 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9067) covalent geometry : angle 0.54472 / 0.28 (12244) hydrogen bonds : bond 0.04287 / 2.97 ( 514) hydrogen bonds : angle 4.36579 / 3.05 ( 1458) Misc. bond : bond 0.00074 / 0.04 ( 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 282 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.6465 (mmm) cc_final: 0.6076 (mmm) REVERT: A 101 LYS cc_start: 0.5994 (tttm) cc_final: 0.5693 (tppt) REVERT: A 131 LYS cc_start: 0.7817 (mttt) cc_final: 0.7266 (mmtm) REVERT: A 194 LEU cc_start: 0.7372 (mt) cc_final: 0.7117 (tt) REVERT: A 215 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7404 (mtm180) REVERT: N 50 TYR cc_start: 0.9206 (p90) cc_final: 0.8850 (p90) REVERT: R 35 ASP cc_start: 0.7440 (t0) cc_final: 0.6935 (t0) REVERT: R 176 GLN cc_start: 0.7959 (mp10) cc_final: 0.7364 (mp10) REVERT: R 210 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7353 (mt) REVERT: S 65 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7629 (mttm) REVERT: S 119 ARG cc_start: 0.8415 (ttp80) cc_final: 0.7894 (ttt-90) REVERT: S 135 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6465 (tm-30) REVERT: T 52 MET cc_start: 0.8061 (mmm) cc_final: 0.7808 (mmm) REVERT: T 81 GLU cc_start: 0.7456 (pm20) cc_final: 0.7175 (pm20) REVERT: T 95 MET cc_start: 0.7914 (tpp) cc_final: 0.7312 (ttt) outliers start: 36 outliers final: 31 residues processed: 263 average time/residue: 0.0871 time to fit residues: 31.7774 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 : 0.315 ------------------------------------------------------------------------------- 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 62 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 204 GLN Chi-restraints excluded: chain A residue 208 SER 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 N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG 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 234 LEU Chi-restraints excluded: chain R residue 298 THR 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 92 LEU Chi-restraints excluded: chain T residue 100 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 T residue 156 LEU Chi-restraints excluded: chain X residue 74 ILE 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: 2.9990 chunk 95 optimal weight: 0.0770 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3760 r_free = 0.3760 target = 0.164570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122030 restraints weight = 11623.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.125934 restraints weight = 6182.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.128585 restraints weight = 3957.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.130407 restraints weight = 2859.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131593 restraints weight = 2230.891| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9069 Z= 0.124 Angle : 0.550 9.560 12244 Z= 0.282 Chirality : 0.041 0.204 1434 Planarity : 0.003 0.042 1579 Dihedral : 4.280 43.104 1254 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.76 % Allowed : 20.19 % Favored : 76.05 % 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: 1.63 (0.24), residues: 1149 helix: 1.85 (0.22), residues: 550 sheet: 1.71 (0.32), residues: 221 loop : -0.45 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.014 0.001 TYR X 61 PHE 0.018 0.001 PHE A 165 TRP 0.020 0.002 TRP A 57 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9067) covalent geometry : angle 0.55037 / 0.28 (12244) hydrogen bonds : bond 0.03997 / 2.76 ( 514) hydrogen bonds : angle 4.27146 / 2.98 ( 1458) Misc. bond : bond 0.00069 / 0.04 ( 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 278 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7423 (mmm) cc_final: 0.7057 (mmt) REVERT: A 82 ASP cc_start: 0.6134 (t0) cc_final: 0.5732 (t0) REVERT: A 101 LYS cc_start: 0.5982 (tttm) cc_final: 0.5711 (tppt) REVERT: A 131 LYS cc_start: 0.7840 (mttt) cc_final: 0.7271 (mmtm) REVERT: A 194 LEU cc_start: 0.7286 (mt) cc_final: 0.7008 (tt) REVERT: A 215 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7344 (mtm180) REVERT: N 50 TYR cc_start: 0.9186 (p90) cc_final: 0.8842 (p90) REVERT: R 35 ASP cc_start: 0.7415 (t0) cc_final: 0.6913 (t0) REVERT: R 111 GLU cc_start: 0.8274 (mp0) cc_final: 0.7901 (mp0) REVERT: R 176 GLN cc_start: 0.7986 (mp10) cc_final: 0.7381 (mp10) REVERT: R 210 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7320 (mt) REVERT: R 277 GLU cc_start: 0.7826 (tt0) cc_final: 0.7030 (mp0) REVERT: S 58 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7764 (mt-10) REVERT: S 65 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7589 (mttm) REVERT: S 119 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7894 (ttt-90) REVERT: T 52 MET cc_start: 0.8020 (mmm) cc_final: 0.7755 (mmm) REVERT: T 95 MET cc_start: 0.7893 (tpp) cc_final: 0.7291 (ttt) outliers start: 35 outliers final: 28 residues processed: 259 average time/residue: 0.0920 time to fit residues: 32.6281 Evaluate side-chains 261 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 38 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 A residue 207 LEU Chi-restraints excluded: chain A residue 208 SER 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 R residue 49 ASP 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 210 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 298 THR 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 147 LEU Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 156 LEU Chi-restraints excluded: chain X residue 74 ILE 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: 0.9980 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.0370 chunk 87 optimal weight: 0.0050 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3786 r_free = 0.3786 target = 0.167227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.124331 restraints weight = 11562.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.128222 restraints weight = 6165.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130879 restraints weight = 3966.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132688 restraints weight = 2874.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.134037 restraints weight = 2259.049| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9069 Z= 0.109 Angle : 0.550 13.644 12244 Z= 0.280 Chirality : 0.040 0.210 1434 Planarity : 0.003 0.044 1579 Dihedral : 4.158 40.634 1254 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.58 % Allowed : 21.27 % Favored : 76.15 % 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: 1.87 (0.24), residues: 1149 helix: 2.10 (0.22), residues: 551 sheet: 1.77 (0.32), residues: 222 loop : -0.41 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.013 0.001 TYR X 61 PHE 0.019 0.001 PHE A 165 TRP 0.026 0.002 TRP A 57 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9067) covalent geometry : angle 0.55045 / 0.28 (12244) hydrogen bonds : bond 0.03606 / 2.49 ( 514) hydrogen bonds : angle 4.15534 / 2.91 ( 1458) Misc. bond : bond 0.00050 / 0.03 ( 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 268 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6931 (ttt90) cc_final: 0.6687 (tpt170) REVERT: A 78 MET cc_start: 0.7472 (mmm) cc_final: 0.7092 (mmt) REVERT: A 101 LYS cc_start: 0.5947 (tttm) cc_final: 0.5683 (tppt) REVERT: A 131 LYS cc_start: 0.7830 (mttt) cc_final: 0.7292 (mmtm) REVERT: A 194 LEU cc_start: 0.7367 (mt) cc_final: 0.7121 (tt) REVERT: A 215 ARG cc_start: 0.7553 (mtm180) cc_final: 0.7217 (ptm160) REVERT: N 50 TYR cc_start: 0.9169 (p90) cc_final: 0.8768 (p90) REVERT: R 35 ASP cc_start: 0.7404 (t0) cc_final: 0.6882 (t0) REVERT: R 111 GLU cc_start: 0.8291 (mp0) cc_final: 0.7915 (mp0) REVERT: R 176 GLN cc_start: 0.8004 (mp10) cc_final: 0.7410 (mp10) REVERT: R 210 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7252 (mt) REVERT: R 277 GLU cc_start: 0.7820 (tt0) cc_final: 0.7007 (mp0) REVERT: R 294 LYS cc_start: 0.7917 (mptt) cc_final: 0.7598 (mptt) REVERT: S 58 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7733 (mt-10) REVERT: S 65 LYS cc_start: 0.7775 (mmtp) cc_final: 0.7557 (mttm) REVERT: S 119 ARG cc_start: 0.8363 (ttp80) cc_final: 0.7881 (ttt-90) REVERT: T 52 MET cc_start: 0.7964 (mmm) cc_final: 0.7674 (mmm) REVERT: T 72 SER cc_start: 0.8575 (m) cc_final: 0.7891 (t) REVERT: T 81 GLU cc_start: 0.7383 (pm20) cc_final: 0.7127 (pm20) REVERT: T 95 MET cc_start: 0.7855 (tpp) cc_final: 0.7262 (ttt) REVERT: X 27 LYS cc_start: 0.7880 (tppp) cc_final: 0.7669 (tppt) outliers start: 24 outliers final: 23 residues processed: 253 average time/residue: 0.0970 time to fit residues: 33.5295 Evaluate side-chains 261 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 38 THR 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 A residue 207 LEU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 49 ASP 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 210 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 298 THR 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 T residue 155 LEU Chi-restraints excluded: chain T residue 156 LEU Chi-restraints excluded: chain X residue 74 ILE 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: 2.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3710 r_free = 0.3710 target = 0.159627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.118122 restraints weight = 11622.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.121634 restraints weight = 6415.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124111 restraints weight = 4213.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.125801 restraints weight = 3072.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.126893 restraints weight = 2436.291| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9069 Z= 0.233 Angle : 0.661 11.657 12244 Z= 0.337 Chirality : 0.044 0.236 1434 Planarity : 0.004 0.038 1579 Dihedral : 4.871 57.796 1254 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.65 % Allowed : 20.41 % Favored : 75.94 % 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: 1.32 (0.24), residues: 1149 helix: 1.53 (0.21), residues: 547 sheet: 1.82 (0.33), residues: 216 loop : -0.61 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 30 TYR 0.013 0.002 TYR X 61 PHE 0.018 0.002 PHE A 165 TRP 0.030 0.003 TRP A 57 HIS 0.006 0.001 HIS O 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 ( 9067) covalent geometry : angle 0.66108 / 0.34 (12244) hydrogen bonds : bond 0.05437 / 3.75 ( 514) hydrogen bonds : angle 4.70717 / 3.27 ( 1458) Misc. bond : bond 0.00095 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1708.97 seconds wall clock time: 30 minutes 3.74 seconds (1803.74 seconds total)