Starting phenix.real_space_refine on Mon May 12 02:58:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhp_61489/05_2025/9jhp_61489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhp_61489/05_2025/9jhp_61489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhp_61489/05_2025/9jhp_61489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhp_61489/05_2025/9jhp_61489.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhp_61489/05_2025/9jhp_61489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhp_61489/05_2025/9jhp_61489.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 55 5.16 5 C 5524 2.51 5 N 1485 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8683 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1745 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "S" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1743 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 401 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2241 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 276} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.06, per 1000 atoms: 0.58 Number of scatterers: 8683 At special positions: 0 Unit cell: (95.04, 121.92, 136.32, 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 55 16.00 O 1619 8.00 N 1485 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.895A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.586A pdb=" N ARG A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.925A pdb=" N THR A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.595A pdb=" N ASP A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.583A pdb=" N LYS A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 228 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.631A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 4.014A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.594A pdb=" N ILE R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.559A pdb=" N ARG R 44 " --> pdb=" O TRP R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 79 removed outlier: 3.848A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 3.764A pdb=" N ASP R 75 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 98 removed outlier: 3.581A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY R 94 " --> pdb=" O CYS R 90 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE R 95 " --> pdb=" O LYS R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 120 removed outlier: 3.823A pdb=" N ALA R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 108 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.757A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 150 through 155' Processing helix chain 'R' and resid 177 through 188 Processing helix chain 'R' and resid 190 through 210 removed outlier: 3.625A pdb=" N LEU R 205 " --> pdb=" O TYR R 201 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 254 removed outlier: 3.944A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 239 - end of helix removed outlier: 3.835A pdb=" N TYR R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 276 removed outlier: 3.850A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA R 273 " --> pdb=" O HIS R 269 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 3.729A pdb=" N PHE A 74 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 35 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU A 107 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 37 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 39 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.789A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.114A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.596A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.908A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.784A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.836A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.639A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.909A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 removed outlier: 3.859A pdb=" N PHE S 213 " --> pdb=" O CYS S 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 167 through 168 removed outlier: 3.670A pdb=" N HIS S 168 " --> pdb=" O ASN S 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN S 172 " --> pdb=" O HIS S 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.890A pdb=" N TRP S 177 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR S 191 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU S 175 " --> pdb=" O TYR S 191 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET S 231 " --> pdb=" O TYR S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 158 through 160 removed outlier: 4.227A pdb=" N PHE R 159 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE R 167 " --> pdb=" O PHE R 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 380 hydrogen bonds defined for protein. 1083 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: 2.24 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2295 1.33 - 1.45: 1785 1.45 - 1.58: 4720 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8876 Sorted by residual: bond pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.33e-02 5.65e+03 5.97e+00 bond pdb=" C MET B 262 " pdb=" N THR B 263 " ideal model delta sigma weight residual 1.331 1.349 -0.019 1.29e-02 6.01e+03 2.07e+00 bond pdb=" C LEU R 70 " pdb=" N PRO R 71 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.80e+00 bond pdb=" C ASP S 74 " pdb=" N PRO S 75 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.56e+00 bond pdb=" CB GLU B 172 " pdb=" CG GLU B 172 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11751 1.76 - 3.53: 237 3.53 - 5.29: 46 5.29 - 7.06: 20 7.06 - 8.82: 5 Bond angle restraints: 12059 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.23 107.31 5.92 1.24e+00 6.50e-01 2.28e+01 angle pdb=" N ASP A 147 " pdb=" CA ASP A 147 " pdb=" C ASP A 147 " ideal model delta sigma weight residual 113.18 107.75 5.43 1.33e+00 5.65e-01 1.67e+01 angle pdb=" CA LYS A 152 " pdb=" CB LYS A 152 " pdb=" CG LYS A 152 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" N LEU R 92 " pdb=" CA LEU R 92 " pdb=" C LEU R 92 " ideal model delta sigma weight residual 112.93 108.82 4.11 1.33e+00 5.65e-01 9.53e+00 angle pdb=" CA MET C 21 " pdb=" CB MET C 21 " pdb=" CG MET C 21 " ideal model delta sigma weight residual 114.10 120.18 -6.08 2.00e+00 2.50e-01 9.24e+00 ... (remaining 12054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 4567 15.91 - 31.82: 482 31.82 - 47.73: 137 47.73 - 63.64: 30 63.64 - 79.54: 7 Dihedral angle restraints: 5223 sinusoidal: 1945 harmonic: 3278 Sorted by residual: dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 180.00 117.39 62.61 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 138.05 -45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS S 160 " pdb=" SG CYS S 160 " pdb=" SG CYS S 230 " pdb=" CB CYS S 230 " ideal model delta sinusoidal sigma weight residual 93.00 56.37 36.63 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 978 0.038 - 0.077: 280 0.077 - 0.115: 96 0.115 - 0.154: 12 0.154 - 0.192: 3 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CG LEU R 72 " pdb=" CB LEU R 72 " pdb=" CD1 LEU R 72 " pdb=" CD2 LEU R 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CG LEU R 92 " pdb=" CB LEU R 92 " pdb=" CD1 LEU R 92 " pdb=" CD2 LEU R 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CB THR S 145 " pdb=" CA THR S 145 " pdb=" OG1 THR S 145 " pdb=" CG2 THR S 145 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 1366 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 172 " -0.070 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO R 173 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO R 173 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO R 173 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO C 53 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.038 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO C 55 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.031 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 880 2.74 - 3.28: 8397 3.28 - 3.82: 13758 3.82 - 4.36: 15748 4.36 - 4.90: 27278 Nonbonded interactions: 66061 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.229 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP A 114 " pdb=" ND2 ASN A 116 " model vdw 2.246 3.120 nonbonded pdb=" O ASN A 116 " pdb=" OG1 THR A 119 " model vdw 2.270 3.040 ... (remaining 66056 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.290 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8879 Z= 0.149 Angle : 0.682 8.822 12065 Z= 0.369 Chirality : 0.041 0.192 1369 Planarity : 0.006 0.109 1539 Dihedral : 14.730 79.544 3100 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 23.18 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1115 helix: 0.62 (0.28), residues: 379 sheet: -0.09 (0.32), residues: 250 loop : -1.69 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 73 HIS 0.003 0.001 HIS B 91 PHE 0.026 0.002 PHE R 192 TYR 0.017 0.001 TYR R 163 ARG 0.008 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.28559 ( 380) hydrogen bonds : angle 8.06928 ( 1083) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.33463 ( 6) covalent geometry : bond 0.00309 ( 8876) covalent geometry : angle 0.68143 (12059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7419 (ttt90) cc_final: 0.7192 (ttt-90) REVERT: B 68 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7512 (mtp180) REVERT: B 155 ASN cc_start: 0.7090 (m-40) cc_final: 0.6419 (t0) REVERT: B 170 ASP cc_start: 0.6945 (t0) cc_final: 0.6572 (t0) REVERT: B 175 GLN cc_start: 0.8183 (mt0) cc_final: 0.7916 (mt0) REVERT: B 225 HIS cc_start: 0.7245 (m-70) cc_final: 0.6860 (m-70) REVERT: S 95 TYR cc_start: 0.8417 (m-10) cc_final: 0.8093 (m-10) REVERT: S 231 MET cc_start: 0.8139 (ttt) cc_final: 0.7937 (ttt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2551 time to fit residues: 78.5341 Evaluate side-chains 234 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 88 ASN S 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120035 restraints weight = 13799.277| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.04 r_work: 0.3443 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8879 Z= 0.146 Angle : 0.623 8.722 12065 Z= 0.325 Chirality : 0.043 0.154 1369 Planarity : 0.005 0.086 1539 Dihedral : 4.465 57.537 1220 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.57 % Allowed : 19.04 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1115 helix: 1.11 (0.27), residues: 388 sheet: -0.28 (0.32), residues: 261 loop : -1.68 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 142 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE B 199 TYR 0.023 0.002 TYR R 102 ARG 0.006 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.05612 ( 380) hydrogen bonds : angle 5.20943 ( 1083) SS BOND : bond 0.00731 ( 3) SS BOND : angle 1.45076 ( 6) covalent geometry : bond 0.00314 ( 8876) covalent geometry : angle 0.62213 (12059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7330 (ttt90) cc_final: 0.7125 (ttt-90) REVERT: A 94 LYS cc_start: 0.8445 (mppt) cc_final: 0.8232 (mppt) REVERT: A 114 ASP cc_start: 0.6568 (t70) cc_final: 0.6244 (t70) REVERT: A 127 THR cc_start: 0.8370 (m) cc_final: 0.8079 (p) REVERT: B 124 TYR cc_start: 0.8001 (m-80) cc_final: 0.7721 (m-80) REVERT: B 155 ASN cc_start: 0.7266 (m-40) cc_final: 0.6770 (t0) REVERT: B 170 ASP cc_start: 0.7226 (t0) cc_final: 0.6850 (t0) REVERT: B 284 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7754 (mt) REVERT: S 50 TYR cc_start: 0.8292 (t80) cc_final: 0.8026 (t80) REVERT: S 93 MET cc_start: 0.6917 (ttp) cc_final: 0.6467 (ttp) REVERT: S 95 TYR cc_start: 0.8412 (m-10) cc_final: 0.7968 (m-10) REVERT: S 141 MET cc_start: 0.7714 (mmt) cc_final: 0.7281 (mmm) REVERT: S 162 SER cc_start: 0.8245 (t) cc_final: 0.8040 (p) REVERT: C 21 MET cc_start: 0.8268 (mmt) cc_final: 0.7924 (mmt) REVERT: C 44 HIS cc_start: 0.8245 (m-70) cc_final: 0.7976 (m90) REVERT: R 227 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7143 (mm) outliers start: 42 outliers final: 26 residues processed: 249 average time/residue: 0.2773 time to fit residues: 89.3913 Evaluate side-chains 251 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 79 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 143 GLN ** 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 = 0.3946 r_free = 0.3946 target = 0.148304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118145 restraints weight = 14104.463| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.08 r_work: 0.3410 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8879 Z= 0.156 Angle : 0.614 9.064 12065 Z= 0.319 Chirality : 0.042 0.145 1369 Planarity : 0.005 0.082 1539 Dihedral : 4.404 55.824 1220 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.81 % Allowed : 19.26 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1115 helix: 1.18 (0.27), residues: 394 sheet: -0.29 (0.31), residues: 272 loop : -1.73 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 142 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.002 PHE B 278 TYR 0.019 0.002 TYR R 102 ARG 0.004 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.05414 ( 380) hydrogen bonds : angle 4.87197 ( 1083) SS BOND : bond 0.00895 ( 3) SS BOND : angle 1.29203 ( 6) covalent geometry : bond 0.00343 ( 8876) covalent geometry : angle 0.61389 (12059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7425 (ttt90) cc_final: 0.7214 (ttt-90) REVERT: A 92 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7288 (tp30) REVERT: A 114 ASP cc_start: 0.6467 (t70) cc_final: 0.6200 (t70) REVERT: A 127 THR cc_start: 0.8343 (m) cc_final: 0.8109 (p) REVERT: B 137 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7958 (mmm-85) REVERT: B 155 ASN cc_start: 0.7333 (m-40) cc_final: 0.6860 (t0) REVERT: B 170 ASP cc_start: 0.7349 (t0) cc_final: 0.6845 (t0) REVERT: B 171 ILE cc_start: 0.7545 (mm) cc_final: 0.7295 (mm) REVERT: B 197 ARG cc_start: 0.7720 (mtm180) cc_final: 0.7488 (mtm-85) REVERT: B 273 ILE cc_start: 0.7814 (mp) cc_final: 0.7563 (mt) REVERT: B 284 LEU cc_start: 0.8127 (mm) cc_final: 0.7825 (mt) REVERT: S 141 MET cc_start: 0.7692 (mmt) cc_final: 0.7477 (mmm) REVERT: S 228 TYR cc_start: 0.7968 (m-80) cc_final: 0.7707 (m-80) REVERT: C 21 MET cc_start: 0.8326 (mmt) cc_final: 0.8007 (mmt) REVERT: C 44 HIS cc_start: 0.8306 (m-70) cc_final: 0.8029 (m-70) REVERT: R 175 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6809 (mt-10) REVERT: R 197 MET cc_start: 0.7651 (ttm) cc_final: 0.7319 (mtp) REVERT: R 227 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7109 (mm) outliers start: 35 outliers final: 25 residues processed: 242 average time/residue: 0.2535 time to fit residues: 79.4339 Evaluate side-chains 249 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 32 GLN B 340 ASN S 143 GLN R 58 ASN R 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118399 restraints weight = 13937.162| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.06 r_work: 0.3423 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8879 Z= 0.134 Angle : 0.576 9.152 12065 Z= 0.300 Chirality : 0.041 0.133 1369 Planarity : 0.005 0.078 1539 Dihedral : 4.361 55.542 1220 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.13 % Allowed : 19.91 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1115 helix: 1.41 (0.27), residues: 395 sheet: -0.21 (0.31), residues: 272 loop : -1.68 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 142 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.002 PHE R 159 TYR 0.023 0.002 TYR R 163 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 380) hydrogen bonds : angle 4.56393 ( 1083) SS BOND : bond 0.00612 ( 3) SS BOND : angle 1.19637 ( 6) covalent geometry : bond 0.00298 ( 8876) covalent geometry : angle 0.57508 (12059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7339 (ttt90) cc_final: 0.7117 (ttt-90) REVERT: B 67 SER cc_start: 0.8631 (m) cc_final: 0.8075 (t) REVERT: B 137 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.7994 (mmm-85) REVERT: B 155 ASN cc_start: 0.7337 (m-40) cc_final: 0.6880 (t0) REVERT: B 170 ASP cc_start: 0.7344 (t0) cc_final: 0.6809 (t0) REVERT: B 197 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7282 (mtm-85) REVERT: B 273 ILE cc_start: 0.7812 (mp) cc_final: 0.7563 (mt) REVERT: B 284 LEU cc_start: 0.8115 (mm) cc_final: 0.7818 (mt) REVERT: S 50 TYR cc_start: 0.8391 (t80) cc_final: 0.8035 (t80) REVERT: C 21 MET cc_start: 0.8367 (mmt) cc_final: 0.8120 (mmt) REVERT: R 181 MET cc_start: 0.6881 (ttt) cc_final: 0.6621 (ttt) REVERT: R 185 ARG cc_start: 0.5851 (ttm110) cc_final: 0.5375 (ttm110) REVERT: R 227 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7207 (mm) outliers start: 38 outliers final: 29 residues processed: 239 average time/residue: 0.2415 time to fit residues: 75.0878 Evaluate side-chains 246 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS B 32 GLN S 39 GLN R 35 ASN R 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117126 restraints weight = 13867.630| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.01 r_work: 0.3409 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8879 Z= 0.159 Angle : 0.604 9.685 12065 Z= 0.314 Chirality : 0.042 0.148 1369 Planarity : 0.005 0.080 1539 Dihedral : 4.473 55.020 1220 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.79 % Allowed : 19.91 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1115 helix: 1.42 (0.27), residues: 396 sheet: -0.20 (0.32), residues: 273 loop : -1.69 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 142 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.002 PHE B 278 TYR 0.022 0.002 TYR R 163 ARG 0.006 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 380) hydrogen bonds : angle 4.59182 ( 1083) SS BOND : bond 0.00678 ( 3) SS BOND : angle 1.24894 ( 6) covalent geometry : bond 0.00360 ( 8876) covalent geometry : angle 0.60371 (12059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7404 (ttt90) cc_final: 0.7183 (ttt-90) REVERT: A 113 SER cc_start: 0.7844 (p) cc_final: 0.7634 (p) REVERT: B 22 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7610 (mmt90) REVERT: B 67 SER cc_start: 0.8633 (m) cc_final: 0.8095 (t) REVERT: B 137 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.7994 (mmm-85) REVERT: B 155 ASN cc_start: 0.7352 (m-40) cc_final: 0.6901 (t0) REVERT: B 170 ASP cc_start: 0.7438 (t0) cc_final: 0.6880 (t0) REVERT: B 197 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7297 (mtm-85) REVERT: B 273 ILE cc_start: 0.7748 (mp) cc_final: 0.7530 (mt) REVERT: B 284 LEU cc_start: 0.8119 (mm) cc_final: 0.7831 (mt) REVERT: S 50 TYR cc_start: 0.8453 (t80) cc_final: 0.8045 (t80) REVERT: C 21 MET cc_start: 0.8393 (mmt) cc_final: 0.8180 (mmt) REVERT: R 227 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7228 (mm) REVERT: R 247 ARG cc_start: 0.7341 (tmm-80) cc_final: 0.6561 (ttm-80) outliers start: 44 outliers final: 37 residues processed: 233 average time/residue: 0.2478 time to fit residues: 74.5344 Evaluate side-chains 252 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS B 32 GLN R 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118955 restraints weight = 13826.081| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.02 r_work: 0.3429 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8879 Z= 0.121 Angle : 0.577 9.231 12065 Z= 0.296 Chirality : 0.041 0.159 1369 Planarity : 0.005 0.079 1539 Dihedral : 4.317 54.975 1220 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.90 % Allowed : 20.89 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1115 helix: 1.57 (0.27), residues: 397 sheet: -0.05 (0.32), residues: 272 loop : -1.60 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 142 HIS 0.003 0.001 HIS B 183 PHE 0.019 0.001 PHE S 213 TYR 0.020 0.001 TYR R 102 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 380) hydrogen bonds : angle 4.38061 ( 1083) SS BOND : bond 0.00654 ( 3) SS BOND : angle 0.89201 ( 6) covalent geometry : bond 0.00267 ( 8876) covalent geometry : angle 0.57666 (12059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7278 (ttt90) cc_final: 0.6860 (ttt180) REVERT: A 124 ASP cc_start: 0.7751 (t0) cc_final: 0.7471 (t0) REVERT: B 22 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7662 (mmt90) REVERT: B 67 SER cc_start: 0.8640 (m) cc_final: 0.8108 (t) REVERT: B 137 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8024 (mmm-85) REVERT: B 155 ASN cc_start: 0.7345 (m-40) cc_final: 0.6939 (t0) REVERT: B 170 ASP cc_start: 0.7465 (t0) cc_final: 0.6883 (t0) REVERT: B 197 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7285 (mtm-85) REVERT: B 273 ILE cc_start: 0.7733 (mp) cc_final: 0.7533 (mt) REVERT: S 50 TYR cc_start: 0.8436 (t80) cc_final: 0.7986 (t80) REVERT: S 141 MET cc_start: 0.7867 (mmm) cc_final: 0.6807 (mmm) REVERT: R 181 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6693 (ttt) REVERT: R 227 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7278 (mm) REVERT: R 247 ARG cc_start: 0.7359 (tmm-80) cc_final: 0.6660 (ttm-80) outliers start: 45 outliers final: 33 residues processed: 237 average time/residue: 0.2622 time to fit residues: 79.7015 Evaluate side-chains 253 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 259 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118005 restraints weight = 13965.487| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.05 r_work: 0.3407 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8879 Z= 0.152 Angle : 0.608 9.184 12065 Z= 0.313 Chirality : 0.042 0.135 1369 Planarity : 0.005 0.078 1539 Dihedral : 4.404 54.627 1220 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.57 % Allowed : 21.33 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1115 helix: 1.53 (0.27), residues: 396 sheet: 0.02 (0.32), residues: 268 loop : -1.70 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 142 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.002 PHE S 213 TYR 0.022 0.002 TYR R 102 ARG 0.007 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 380) hydrogen bonds : angle 4.46262 ( 1083) SS BOND : bond 0.00648 ( 3) SS BOND : angle 1.20416 ( 6) covalent geometry : bond 0.00346 ( 8876) covalent geometry : angle 0.60779 (12059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7397 (ttt90) cc_final: 0.7182 (ttt-90) REVERT: B 22 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7614 (mmt90) REVERT: B 32 GLN cc_start: 0.8272 (pt0) cc_final: 0.8006 (pm20) REVERT: B 67 SER cc_start: 0.8650 (m) cc_final: 0.8112 (t) REVERT: B 137 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8064 (mmm-85) REVERT: B 155 ASN cc_start: 0.7389 (m-40) cc_final: 0.6941 (t0) REVERT: B 170 ASP cc_start: 0.7515 (t0) cc_final: 0.6901 (t0) REVERT: B 197 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7282 (mtm-85) REVERT: B 234 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 284 LEU cc_start: 0.8146 (mm) cc_final: 0.7799 (mt) REVERT: S 141 MET cc_start: 0.7955 (mmm) cc_final: 0.6811 (mmm) REVERT: R 185 ARG cc_start: 0.5803 (ttm110) cc_final: 0.5578 (ttm110) REVERT: R 197 MET cc_start: 0.7826 (mtp) cc_final: 0.7612 (mtp) REVERT: R 227 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7261 (mm) REVERT: R 247 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.6651 (ttm-80) outliers start: 42 outliers final: 35 residues processed: 232 average time/residue: 0.2502 time to fit residues: 74.6669 Evaluate side-chains 246 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.148003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118169 restraints weight = 14081.324| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.06 r_work: 0.3421 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8879 Z= 0.138 Angle : 0.601 9.197 12065 Z= 0.310 Chirality : 0.042 0.139 1369 Planarity : 0.005 0.078 1539 Dihedral : 4.386 54.422 1220 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.79 % Allowed : 21.65 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1115 helix: 1.58 (0.27), residues: 396 sheet: 0.03 (0.32), residues: 270 loop : -1.67 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 142 HIS 0.003 0.001 HIS B 183 PHE 0.028 0.002 PHE S 213 TYR 0.023 0.001 TYR R 102 ARG 0.007 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 380) hydrogen bonds : angle 4.41856 ( 1083) SS BOND : bond 0.00636 ( 3) SS BOND : angle 1.22092 ( 6) covalent geometry : bond 0.00312 ( 8876) covalent geometry : angle 0.60027 (12059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7373 (ttt90) cc_final: 0.7152 (ttt-90) REVERT: A 178 PHE cc_start: 0.7485 (t80) cc_final: 0.7236 (t80) REVERT: B 22 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7622 (mmt90) REVERT: B 67 SER cc_start: 0.8637 (m) cc_final: 0.8110 (t) REVERT: B 137 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8039 (mmm-85) REVERT: B 155 ASN cc_start: 0.7389 (m-40) cc_final: 0.6953 (t0) REVERT: B 170 ASP cc_start: 0.7521 (t0) cc_final: 0.6920 (t0) REVERT: B 197 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7301 (mtm-85) REVERT: B 234 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: S 141 MET cc_start: 0.7958 (mmm) cc_final: 0.6978 (mmm) REVERT: R 227 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7203 (mm) outliers start: 44 outliers final: 35 residues processed: 226 average time/residue: 0.2476 time to fit residues: 72.2073 Evaluate side-chains 241 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118449 restraints weight = 14078.895| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.13 r_work: 0.3419 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8879 Z= 0.123 Angle : 0.609 9.109 12065 Z= 0.310 Chirality : 0.041 0.137 1369 Planarity : 0.004 0.079 1539 Dihedral : 4.311 54.177 1220 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.35 % Allowed : 21.98 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1115 helix: 1.59 (0.27), residues: 396 sheet: 0.11 (0.32), residues: 268 loop : -1.64 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 142 HIS 0.003 0.001 HIS B 183 PHE 0.029 0.002 PHE S 213 TYR 0.019 0.001 TYR R 102 ARG 0.006 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 380) hydrogen bonds : angle 4.34231 ( 1083) SS BOND : bond 0.00586 ( 3) SS BOND : angle 1.23012 ( 6) covalent geometry : bond 0.00274 ( 8876) covalent geometry : angle 0.60850 (12059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7299 (ttt90) cc_final: 0.7080 (ttt-90) REVERT: A 178 PHE cc_start: 0.7396 (t80) cc_final: 0.7170 (t80) REVERT: B 22 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7642 (mmt90) REVERT: B 67 SER cc_start: 0.8633 (m) cc_final: 0.8166 (p) REVERT: B 137 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8050 (mmm-85) REVERT: B 155 ASN cc_start: 0.7390 (m-40) cc_final: 0.6960 (t0) REVERT: B 170 ASP cc_start: 0.7525 (t0) cc_final: 0.6902 (t0) REVERT: B 197 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7298 (mtm-85) REVERT: B 234 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: R 197 MET cc_start: 0.7966 (ttp) cc_final: 0.7649 (ttm) REVERT: R 227 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7202 (mm) outliers start: 40 outliers final: 34 residues processed: 224 average time/residue: 0.2573 time to fit residues: 74.2993 Evaluate side-chains 237 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119694 restraints weight = 14098.389| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.08 r_work: 0.3448 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8879 Z= 0.104 Angle : 0.592 9.039 12065 Z= 0.298 Chirality : 0.041 0.136 1369 Planarity : 0.004 0.079 1539 Dihedral : 4.160 53.423 1220 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.94 % Allowed : 23.72 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1115 helix: 1.67 (0.27), residues: 397 sheet: 0.19 (0.32), residues: 263 loop : -1.55 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.032 0.001 PHE S 213 TYR 0.014 0.001 TYR R 102 ARG 0.006 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 380) hydrogen bonds : angle 4.13903 ( 1083) SS BOND : bond 0.00447 ( 3) SS BOND : angle 1.00848 ( 6) covalent geometry : bond 0.00225 ( 8876) covalent geometry : angle 0.59183 (12059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7125 (ttt90) cc_final: 0.6806 (ttt180) REVERT: A 178 PHE cc_start: 0.7351 (t80) cc_final: 0.7085 (t80) REVERT: B 22 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7662 (mmt90) REVERT: B 67 SER cc_start: 0.8609 (m) cc_final: 0.8187 (p) REVERT: B 137 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8045 (mmm-85) REVERT: B 155 ASN cc_start: 0.7410 (m-40) cc_final: 0.7016 (t0) REVERT: B 170 ASP cc_start: 0.7494 (t0) cc_final: 0.6874 (t0) REVERT: B 234 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: B 273 ILE cc_start: 0.7705 (mp) cc_final: 0.7466 (mt) REVERT: S 96 CYS cc_start: 0.8434 (t) cc_final: 0.7545 (p) REVERT: R 167 PHE cc_start: 0.5510 (m-10) cc_final: 0.5204 (m-10) REVERT: R 197 MET cc_start: 0.7921 (ttp) cc_final: 0.7691 (ttm) outliers start: 27 outliers final: 21 residues processed: 216 average time/residue: 0.2609 time to fit residues: 72.5440 Evaluate side-chains 222 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 8 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119915 restraints weight = 13986.394| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.06 r_work: 0.3448 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8879 Z= 0.112 Angle : 0.603 9.038 12065 Z= 0.302 Chirality : 0.041 0.137 1369 Planarity : 0.004 0.079 1539 Dihedral : 4.137 53.207 1220 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.05 % Allowed : 23.29 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1115 helix: 1.71 (0.27), residues: 398 sheet: 0.27 (0.32), residues: 264 loop : -1.50 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 221 PHE 0.034 0.001 PHE S 213 TYR 0.022 0.001 TYR S 95 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 380) hydrogen bonds : angle 4.12323 ( 1083) SS BOND : bond 0.00576 ( 3) SS BOND : angle 1.09921 ( 6) covalent geometry : bond 0.00249 ( 8876) covalent geometry : angle 0.60261 (12059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4633.94 seconds wall clock time: 80 minutes 59.40 seconds (4859.40 seconds total)