Starting phenix.real_space_refine on Tue Apr 29 12:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhp_61489/04_2025/9jhp_61489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhp_61489/04_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_61489/04_2025/9jhp_61489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhp_61489/04_2025/9jhp_61489.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhp_61489/04_2025/9jhp_61489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhp_61489/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.19, per 1000 atoms: 0.60 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: 2.03 Conformation dependent library (CDL) restraints added in 982.3 milliseconds 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: 1.00 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: 2.42 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: 1.230 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.770 Find NCS groups from input model: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- 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 : 0.884 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: 0.2593 time to fit residues: 79.9434 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 : 0.882 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.149856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120006 restraints weight = 13803.871| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.03 r_work: 0.3442 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 5.99 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 5.20951 ( 1083) SS BOND : bond 0.00731 ( 3) SS BOND : angle 1.45066 ( 6) covalent geometry : bond 0.00314 ( 8876) covalent geometry : angle 0.62212 (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 : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7333 (ttt90) cc_final: 0.7129 (ttt-90) REVERT: A 94 LYS cc_start: 0.8447 (mppt) cc_final: 0.8234 (mppt) REVERT: A 114 ASP cc_start: 0.6572 (t70) cc_final: 0.6247 (t70) REVERT: A 127 THR cc_start: 0.8368 (m) cc_final: 0.8077 (p) REVERT: B 124 TYR cc_start: 0.8002 (m-80) cc_final: 0.7722 (m-80) REVERT: B 155 ASN cc_start: 0.7266 (m-40) cc_final: 0.6776 (t0) REVERT: B 170 ASP cc_start: 0.7225 (t0) cc_final: 0.6852 (t0) REVERT: B 284 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7749 (mt) REVERT: S 50 TYR cc_start: 0.8293 (t80) cc_final: 0.8027 (t80) REVERT: S 93 MET cc_start: 0.6907 (ttp) cc_final: 0.6462 (ttp) REVERT: S 95 TYR cc_start: 0.8412 (m-10) cc_final: 0.7968 (m-10) REVERT: S 141 MET cc_start: 0.7712 (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: 0.8250 (mmt) cc_final: 0.7912 (mmt) REVERT: C 44 HIS cc_start: 0.8244 (m-70) cc_final: 0.7975 (m90) REVERT: R 227 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7147 (mm) outliers start: 42 outliers final: 26 residues processed: 249 average time/residue: 0.2705 time to fit residues: 87.9283 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 : 0.916 ------------------------------------------------------------------------------- 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: 0.5980 chunk 79 optimal weight: 0.9980 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: 0.6980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.147594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117647 restraints weight = 14096.106| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.03 r_work: 0.3402 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8879 Z= 0.178 Angle : 0.635 9.131 12065 Z= 0.331 Chirality : 0.043 0.150 1369 Planarity : 0.005 0.082 1539 Dihedral : 4.497 55.942 1220 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.92 % Allowed : 19.26 % 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: -0.56 (0.25), residues: 1115 helix: 1.10 (0.27), residues: 395 sheet: -0.24 (0.32), residues: 268 loop : -1.79 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 142 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.002 PHE B 278 TYR 0.018 0.002 TYR R 102 ARG 0.007 0.001 ARG R 247 Details of bonding type rmsd hydrogen bonds : bond 0.05738 ( 380) hydrogen bonds : angle 4.98496 ( 1083) SS BOND : bond 0.00599 ( 3) SS BOND : angle 1.47656 ( 6) covalent geometry : bond 0.00401 ( 8876) covalent geometry : angle 0.63471 (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 267 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7464 (ttt90) cc_final: 0.7249 (ttt-90) REVERT: A 114 ASP cc_start: 0.6532 (t70) cc_final: 0.6173 (t70) REVERT: A 127 THR cc_start: 0.8365 (m) cc_final: 0.8097 (p) REVERT: B 137 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.7950 (mmm-85) REVERT: B 155 ASN cc_start: 0.7328 (m-40) cc_final: 0.6849 (t0) REVERT: B 170 ASP cc_start: 0.7384 (t0) cc_final: 0.6909 (t0) REVERT: B 171 ILE cc_start: 0.7546 (mm) cc_final: 0.7284 (mm) REVERT: B 197 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7288 (mtm-85) REVERT: B 273 ILE cc_start: 0.7817 (mp) cc_final: 0.7564 (mt) REVERT: B 284 LEU cc_start: 0.8136 (mm) cc_final: 0.7831 (mt) REVERT: B 320 VAL cc_start: 0.8536 (t) cc_final: 0.8326 (p) REVERT: S 109 ASP cc_start: 0.7832 (p0) cc_final: 0.7629 (p0) REVERT: S 141 MET cc_start: 0.7631 (mmt) cc_final: 0.7393 (mmm) REVERT: C 21 MET cc_start: 0.8277 (mmt) cc_final: 0.7984 (mmt) REVERT: R 175 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6885 (mt-10) REVERT: R 197 MET cc_start: 0.7689 (ttm) cc_final: 0.7345 (mtp) REVERT: R 227 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7128 (mm) outliers start: 36 outliers final: 25 residues processed: 244 average time/residue: 0.3927 time to fit residues: 125.3026 Evaluate side-chains 252 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 233 CYS 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 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: 2.9990 chunk 109 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118555 restraints weight = 13980.476| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.03 r_work: 0.3425 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2148 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= 0.134 Angle : 0.579 9.176 12065 Z= 0.304 Chirality : 0.042 0.134 1369 Planarity : 0.005 0.079 1539 Dihedral : 4.408 55.572 1220 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.24 % Allowed : 19.15 % Favored : 76.61 % 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: -0.40 (0.25), residues: 1115 helix: 1.32 (0.27), residues: 395 sheet: -0.25 (0.31), residues: 271 loop : -1.72 (0.26), residues: 449 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 0.021 0.002 TYR R 163 ARG 0.009 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 380) hydrogen bonds : angle 4.62852 ( 1083) SS BOND : bond 0.00718 ( 3) SS BOND : angle 1.14392 ( 6) covalent geometry : bond 0.00295 ( 8876) covalent geometry : angle 0.57867 (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 267 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7338 (ttt90) cc_final: 0.7112 (ttt-90) REVERT: A 113 SER cc_start: 0.7886 (p) cc_final: 0.7675 (p) REVERT: A 127 THR cc_start: 0.8311 (m) cc_final: 0.8098 (p) REVERT: B 67 SER cc_start: 0.8623 (m) cc_final: 0.8071 (t) REVERT: B 137 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.7981 (mmm-85) REVERT: B 155 ASN cc_start: 0.7326 (m-40) cc_final: 0.6876 (t0) REVERT: B 170 ASP cc_start: 0.7367 (t0) cc_final: 0.6844 (t0) REVERT: B 273 ILE cc_start: 0.7810 (mp) cc_final: 0.7569 (mt) REVERT: B 284 LEU cc_start: 0.8111 (mm) cc_final: 0.7814 (mt) REVERT: S 50 TYR cc_start: 0.8390 (t80) cc_final: 0.7983 (t80) REVERT: C 21 MET cc_start: 0.8372 (mmt) cc_final: 0.8116 (mmt) REVERT: R 185 ARG cc_start: 0.5842 (ttm110) cc_final: 0.5395 (ttm110) REVERT: R 227 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7175 (mm) outliers start: 39 outliers final: 29 residues processed: 244 average time/residue: 0.2578 time to fit residues: 81.3913 Evaluate side-chains 250 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 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 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 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=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: 0.0980 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN S 39 GLN R 35 ASN R 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119183 restraints weight = 13934.237| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.05 r_work: 0.3439 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8879 Z= 0.113 Angle : 0.561 9.558 12065 Z= 0.289 Chirality : 0.041 0.172 1369 Planarity : 0.005 0.082 1539 Dihedral : 4.249 54.726 1220 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.92 % Allowed : 19.91 % Favored : 76.17 % 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: -0.13 (0.25), residues: 1115 helix: 1.55 (0.27), residues: 397 sheet: 0.03 (0.32), residues: 256 loop : -1.64 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 142 HIS 0.002 0.001 HIS B 183 PHE 0.012 0.001 PHE S 27 TYR 0.019 0.001 TYR R 163 ARG 0.007 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 380) hydrogen bonds : angle 4.34930 ( 1083) SS BOND : bond 0.00482 ( 3) SS BOND : angle 0.99553 ( 6) covalent geometry : bond 0.00241 ( 8876) covalent geometry : angle 0.56041 (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 255 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7204 (ttt90) cc_final: 0.6846 (ttt180) REVERT: B 22 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7576 (mmt90) REVERT: B 67 SER cc_start: 0.8620 (m) cc_final: 0.8094 (t) REVERT: B 137 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7960 (mmm-85) REVERT: B 155 ASN cc_start: 0.7361 (m-40) cc_final: 0.6900 (t0) REVERT: B 170 ASP cc_start: 0.7392 (t0) cc_final: 0.6836 (t0) REVERT: B 197 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7199 (mtp-110) REVERT: B 273 ILE cc_start: 0.7699 (mp) cc_final: 0.7491 (mt) REVERT: S 50 TYR cc_start: 0.8399 (t80) cc_final: 0.8019 (t80) REVERT: C 21 MET cc_start: 0.8386 (mmt) cc_final: 0.8166 (mmt) REVERT: R 227 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7254 (mm) REVERT: R 247 ARG cc_start: 0.7336 (tmm-80) cc_final: 0.6662 (ttm-80) outliers start: 36 outliers final: 27 residues processed: 232 average time/residue: 0.2673 time to fit residues: 79.5775 Evaluate side-chains 242 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 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 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 36 CYS Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 137 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 69 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120427 restraints weight = 13864.105| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.02 r_work: 0.3457 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8879 Z= 0.108 Angle : 0.556 9.324 12065 Z= 0.285 Chirality : 0.041 0.174 1369 Planarity : 0.004 0.080 1539 Dihedral : 4.184 54.498 1220 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.35 % Allowed : 20.24 % Favored : 75.41 % 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: 0.13 (0.25), residues: 1115 helix: 1.80 (0.27), residues: 390 sheet: 0.19 (0.32), residues: 255 loop : -1.49 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 142 HIS 0.004 0.001 HIS A 221 PHE 0.018 0.001 PHE S 213 TYR 0.017 0.001 TYR R 102 ARG 0.005 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 380) hydrogen bonds : angle 4.23770 ( 1083) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.87623 ( 6) covalent geometry : bond 0.00236 ( 8876) covalent geometry : angle 0.55615 (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 254 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7144 (ttt90) cc_final: 0.6812 (ttt180) REVERT: A 20 ASP cc_start: 0.7437 (t0) cc_final: 0.7236 (t0) REVERT: A 124 ASP cc_start: 0.7830 (t0) cc_final: 0.7551 (t0) REVERT: B 22 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7637 (mmt90) REVERT: B 67 SER cc_start: 0.8619 (m) cc_final: 0.8099 (t) REVERT: B 137 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8020 (mmm-85) REVERT: B 155 ASN cc_start: 0.7391 (m-40) cc_final: 0.6951 (t0) REVERT: B 170 ASP cc_start: 0.7419 (t0) cc_final: 0.6856 (t0) REVERT: B 253 PHE cc_start: 0.8130 (m-80) cc_final: 0.7891 (m-80) REVERT: B 273 ILE cc_start: 0.7724 (mp) cc_final: 0.7512 (mt) REVERT: S 50 TYR cc_start: 0.8400 (t80) cc_final: 0.8000 (t80) REVERT: S 109 ASP cc_start: 0.7770 (p0) cc_final: 0.7566 (p0) REVERT: S 141 MET cc_start: 0.7880 (mmm) cc_final: 0.7587 (mmm) REVERT: R 185 ARG cc_start: 0.5414 (ttm110) cc_final: 0.5196 (ttm110) REVERT: R 227 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7198 (mm) REVERT: R 247 ARG cc_start: 0.7304 (tmm-80) cc_final: 0.6670 (ttm-80) outliers start: 40 outliers final: 30 residues processed: 231 average time/residue: 0.2617 time to fit residues: 77.9495 Evaluate side-chains 235 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 164 GLU Chi-restraints excluded: chain A residue 220 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 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 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 128 LEU Chi-restraints excluded: chain R residue 149 ASN 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: 5.9990 chunk 106 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 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 = 0.3943 r_free = 0.3943 target = 0.147936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117998 restraints weight = 13919.781| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.03 r_work: 0.3415 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2630 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= 0.147 Angle : 0.597 9.296 12065 Z= 0.307 Chirality : 0.042 0.148 1369 Planarity : 0.005 0.079 1539 Dihedral : 4.326 54.323 1220 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.46 % Allowed : 20.78 % Favored : 74.76 % 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: -0.03 (0.25), residues: 1115 helix: 1.61 (0.27), residues: 397 sheet: 0.11 (0.32), residues: 270 loop : -1.63 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 142 HIS 0.004 0.001 HIS B 183 PHE 0.025 0.002 PHE S 213 TYR 0.017 0.002 TYR R 102 ARG 0.005 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 380) hydrogen bonds : angle 4.38921 ( 1083) SS BOND : bond 0.00637 ( 3) SS BOND : angle 1.29514 ( 6) covalent geometry : bond 0.00333 ( 8876) covalent geometry : angle 0.59602 (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: 41 poor density : 214 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7368 (ttt90) cc_final: 0.7152 (ttt-90) REVERT: A 20 ASP cc_start: 0.7459 (t0) cc_final: 0.7244 (t0) REVERT: A 113 SER cc_start: 0.7718 (p) cc_final: 0.7507 (p) REVERT: A 124 ASP cc_start: 0.7826 (t0) cc_final: 0.7372 (t0) REVERT: B 22 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7630 (mmt90) REVERT: B 32 GLN cc_start: 0.8283 (pt0) cc_final: 0.8032 (pm20) REVERT: B 48 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7770 (mmt-90) REVERT: B 67 SER cc_start: 0.8651 (m) cc_final: 0.8129 (t) REVERT: B 137 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: B 155 ASN cc_start: 0.7402 (m-40) cc_final: 0.6927 (t0) REVERT: B 170 ASP cc_start: 0.7509 (t0) cc_final: 0.6928 (t0) REVERT: B 197 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7194 (mtp-110) REVERT: B 284 LEU cc_start: 0.8104 (mm) cc_final: 0.7748 (mt) REVERT: S 50 TYR cc_start: 0.8462 (t80) cc_final: 0.7991 (t80) REVERT: S 141 MET cc_start: 0.7921 (mmm) cc_final: 0.6819 (mmm) REVERT: R 185 ARG cc_start: 0.5380 (ttm110) cc_final: 0.5010 (ttp-170) REVERT: R 227 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7240 (mm) REVERT: R 247 ARG cc_start: 0.7354 (tmm-80) cc_final: 0.6645 (ttm-80) outliers start: 41 outliers final: 32 residues processed: 233 average time/residue: 0.2610 time to fit residues: 78.4050 Evaluate side-chains 237 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 164 GLU 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 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 112 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 89 optimal weight: 0.0030 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.146869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116834 restraints weight = 14072.961| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.06 r_work: 0.3395 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8879 Z= 0.173 Angle : 0.633 9.240 12065 Z= 0.325 Chirality : 0.043 0.156 1369 Planarity : 0.005 0.078 1539 Dihedral : 4.484 54.474 1220 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.46 % Allowed : 22.31 % Favored : 73.23 % 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: -0.12 (0.25), residues: 1115 helix: 1.54 (0.27), residues: 397 sheet: 0.05 (0.32), residues: 269 loop : -1.69 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 142 HIS 0.004 0.001 HIS B 91 PHE 0.029 0.002 PHE S 213 TYR 0.018 0.002 TYR R 240 ARG 0.005 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 380) hydrogen bonds : angle 4.53614 ( 1083) SS BOND : bond 0.00785 ( 3) SS BOND : angle 1.44345 ( 6) covalent geometry : bond 0.00397 ( 8876) covalent geometry : angle 0.63214 (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 241 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8625 (mppt) cc_final: 0.8310 (mppt) REVERT: A 113 SER cc_start: 0.7713 (p) cc_final: 0.7493 (p) REVERT: B 22 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7637 (mmt90) REVERT: B 48 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7731 (mmt-90) REVERT: B 67 SER cc_start: 0.8641 (m) cc_final: 0.8186 (p) REVERT: B 137 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.7952 (mmm-85) REVERT: B 155 ASN cc_start: 0.7351 (m-40) cc_final: 0.6932 (t0) REVERT: B 170 ASP cc_start: 0.7555 (t0) cc_final: 0.6975 (t0) REVERT: B 197 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7236 (mtp-110) REVERT: B 229 ILE cc_start: 0.7935 (mt) cc_final: 0.7475 (tt) REVERT: B 234 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 284 LEU cc_start: 0.8137 (mm) cc_final: 0.7794 (mt) REVERT: R 185 ARG cc_start: 0.5552 (ttm110) cc_final: 0.5193 (ttp-170) REVERT: R 227 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7179 (mm) outliers start: 41 outliers final: 35 residues processed: 216 average time/residue: 0.2933 time to fit residues: 82.7697 Evaluate side-chains 236 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 149 LEU Chi-restraints excluded: chain A residue 164 GLU 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 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 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 112 SER 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 Chi-restraints excluded: chain R residue 285 LEU 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: 5.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.148652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118568 restraints weight = 14093.961| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.06 r_work: 0.3420 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8879 Z= 0.122 Angle : 0.603 9.125 12065 Z= 0.307 Chirality : 0.042 0.145 1369 Planarity : 0.004 0.080 1539 Dihedral : 4.300 53.724 1220 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.81 % Allowed : 23.50 % Favored : 72.69 % 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: -0.03 (0.25), residues: 1115 helix: 1.61 (0.27), residues: 398 sheet: 0.13 (0.32), residues: 270 loop : -1.65 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 142 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE A 74 TYR 0.014 0.001 TYR S 191 ARG 0.004 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 380) hydrogen bonds : angle 4.32545 ( 1083) SS BOND : bond 0.00542 ( 3) SS BOND : angle 1.08811 ( 6) covalent geometry : bond 0.00272 ( 8876) covalent geometry : angle 0.60300 (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 232 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6886 (ttt-90) REVERT: A 113 SER cc_start: 0.7733 (p) cc_final: 0.7513 (p) REVERT: A 193 LYS cc_start: 0.7050 (mmmm) cc_final: 0.6802 (mmmm) REVERT: B 22 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7651 (mmt90) REVERT: B 48 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.7730 (mmt-90) REVERT: B 67 SER cc_start: 0.8636 (m) cc_final: 0.8182 (p) REVERT: B 137 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7939 (mmm-85) REVERT: B 155 ASN cc_start: 0.7347 (m-40) cc_final: 0.6923 (t0) REVERT: B 170 ASP cc_start: 0.7543 (t0) cc_final: 0.6947 (t0) REVERT: B 197 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7170 (mtp-110) REVERT: B 229 ILE cc_start: 0.7889 (mt) cc_final: 0.7431 (tt) REVERT: B 234 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: S 18 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7328 (tpp80) REVERT: S 95 TYR cc_start: 0.8415 (m-10) cc_final: 0.8101 (m-10) REVERT: R 185 ARG cc_start: 0.5530 (ttm110) cc_final: 0.5168 (ttp-170) REVERT: R 227 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7259 (mm) outliers start: 35 outliers final: 30 residues processed: 212 average time/residue: 0.2893 time to fit residues: 81.0840 Evaluate side-chains 226 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 164 GLU 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 190 LEU Chi-restraints excluded: chain B residue 198 LEU 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 20 LYS 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 111 ILE Chi-restraints excluded: chain R residue 112 SER 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 Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 73 optimal weight: 0.0970 chunk 83 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.150106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119894 restraints weight = 14108.471| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.12 r_work: 0.3440 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 8879 Z= 0.107 Angle : 0.582 9.036 12065 Z= 0.293 Chirality : 0.041 0.156 1369 Planarity : 0.004 0.080 1539 Dihedral : 4.113 53.189 1220 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.59 % Allowed : 23.94 % Favored : 72.47 % 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: 0.14 (0.26), residues: 1115 helix: 1.76 (0.27), residues: 397 sheet: 0.24 (0.32), residues: 265 loop : -1.57 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.028 0.001 PHE S 213 TYR 0.014 0.001 TYR S 191 ARG 0.004 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 380) hydrogen bonds : angle 4.12131 ( 1083) SS BOND : bond 0.00469 ( 3) SS BOND : angle 0.83496 ( 6) covalent geometry : bond 0.00236 ( 8876) covalent geometry : angle 0.58202 (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 233 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7044 (ttt-90) cc_final: 0.6820 (ttt180) REVERT: A 94 LYS cc_start: 0.8616 (mppt) cc_final: 0.8397 (mppt) REVERT: A 113 SER cc_start: 0.7630 (p) cc_final: 0.7425 (p) REVERT: A 193 LYS cc_start: 0.7181 (mmmm) cc_final: 0.6974 (mmmm) REVERT: B 22 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7694 (mmt90) REVERT: B 48 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7664 (mmt-90) REVERT: B 67 SER cc_start: 0.8623 (m) cc_final: 0.8190 (p) REVERT: B 137 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.7762 (mmm-85) REVERT: B 155 ASN cc_start: 0.7424 (m-40) cc_final: 0.6995 (t0) REVERT: B 170 ASP cc_start: 0.7525 (t0) cc_final: 0.6929 (t0) REVERT: B 234 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: R 185 ARG cc_start: 0.5447 (ttm110) cc_final: 0.5106 (ttp-170) REVERT: R 186 VAL cc_start: 0.6210 (t) cc_final: 0.5893 (p) outliers start: 33 outliers final: 27 residues processed: 213 average time/residue: 0.2485 time to fit residues: 69.3668 Evaluate side-chains 224 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 149 LEU 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 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 13 GLN 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 20 LYS 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 112 SER 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: 0.8980 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118789 restraints weight = 13978.012| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.09 r_work: 0.3423 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8879 Z= 0.132 Angle : 0.608 9.096 12065 Z= 0.308 Chirality : 0.042 0.149 1369 Planarity : 0.005 0.080 1539 Dihedral : 4.202 53.126 1220 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.70 % Allowed : 23.94 % Favored : 72.36 % 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: 0.12 (0.25), residues: 1115 helix: 1.70 (0.27), residues: 398 sheet: 0.26 (0.32), residues: 268 loop : -1.58 (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 A 221 PHE 0.032 0.002 PHE S 213 TYR 0.014 0.001 TYR A 29 ARG 0.004 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 380) hydrogen bonds : angle 4.19754 ( 1083) SS BOND : bond 0.00605 ( 3) SS BOND : angle 1.13077 ( 6) covalent geometry : bond 0.00300 ( 8876) covalent geometry : angle 0.60774 (12059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4991.88 seconds wall clock time: 87 minutes 45.95 seconds (5265.95 seconds total)