Starting phenix.real_space_refine on Sun Aug 24 05:59:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uz2_42831/08_2025/8uz2_42831_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uz2_42831/08_2025/8uz2_42831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uz2_42831/08_2025/8uz2_42831_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uz2_42831/08_2025/8uz2_42831_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uz2_42831/08_2025/8uz2_42831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uz2_42831/08_2025/8uz2_42831.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.041 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 2 5.21 5 S 126 5.16 5 C 10976 2.51 5 N 3082 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17474 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2452 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 584 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "C" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3433 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 424} Chain: "D" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2173 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 267} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2452 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain: "F" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 584 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "G" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3433 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 424} Chain: "H" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2006 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6679 SG CYS D 27 93.944 53.701 72.746 1.00103.00 S ATOM 6699 SG CYS D 30 92.802 56.429 70.545 1.00125.69 S ATOM 6830 SG CYS D 46 91.590 52.761 69.812 1.00105.65 S ATOM 6852 SG CYS D 49 95.106 53.826 69.190 1.00111.30 S ATOM 15154 SG CYS H 27 160.541 46.311 53.352 1.00 65.13 S ATOM 15174 SG CYS H 30 162.346 49.018 55.320 1.00 64.18 S ATOM 15305 SG CYS H 46 162.866 45.312 56.276 1.00 81.53 S ATOM 15327 SG CYS H 49 159.705 47.112 57.048 1.00 72.60 S Time building chain proxies: 4.48, per 1000 atoms: 0.26 Number of scatterers: 17474 At special positions: 0 Unit cell: (185.526, 135.976, 127.909, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 126 16.00 P 10 15.00 Mg 2 11.99 O 3276 8.00 N 3082 7.00 C 10976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 833.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 27 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 30 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 30 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 49 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 27 " Number of angles added : 12 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 25 sheets defined 43.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 9 through 27 Processing helix chain 'A' and resid 32 through 55 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 123 through 130 removed outlier: 3.644A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 136 through 153 removed outlier: 3.626A pdb=" N TYR A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.850A pdb=" N SER A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 243 through 252 removed outlier: 3.608A pdb=" N GLY A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 278 through 296 Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 39 through 45 Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.563A pdb=" N ASP C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 177 through 194 Processing helix chain 'C' and resid 249 through 267 Processing helix chain 'C' and resid 296 through 305 removed outlier: 4.394A pdb=" N THR C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 394 through 409 Processing helix chain 'C' and resid 417 through 427 removed outlier: 3.824A pdb=" N GLN C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 433 Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'D' and resid 36 through 42 Processing helix chain 'D' and resid 56 through 65 Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 135 through 152 Processing helix chain 'D' and resid 166 through 169 Processing helix chain 'D' and resid 170 through 187 removed outlier: 3.643A pdb=" N LEU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.593A pdb=" N SER D 207 " --> pdb=" O MET D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 4.343A pdb=" N GLY D 214 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 238 Processing helix chain 'D' and resid 247 through 255 removed outlier: 3.613A pdb=" N GLU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'E' and resid 9 through 27 Processing helix chain 'E' and resid 32 through 55 Processing helix chain 'E' and resid 59 through 68 Processing helix chain 'E' and resid 74 through 83 Processing helix chain 'E' and resid 123 through 130 removed outlier: 3.619A pdb=" N ILE E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 136 through 153 removed outlier: 3.583A pdb=" N TYR E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS E 142 " --> pdb=" O GLU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 175 Processing helix chain 'E' and resid 176 through 189 removed outlier: 3.840A pdb=" N SER E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 229 through 238 Processing helix chain 'E' and resid 243 through 252 removed outlier: 3.546A pdb=" N GLY E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 278 through 299 removed outlier: 4.296A pdb=" N VAL E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 315 Processing helix chain 'G' and resid 11 through 25 Processing helix chain 'G' and resid 39 through 45 Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 88 through 98 removed outlier: 3.758A pdb=" N SER G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.854A pdb=" N ASP G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 127 removed outlier: 3.640A pdb=" N ALA G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 Processing helix chain 'G' and resid 174 through 176 No H-bonds generated for 'chain 'G' and resid 174 through 176' Processing helix chain 'G' and resid 177 through 194 removed outlier: 3.578A pdb=" N SER G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 267 removed outlier: 3.544A pdb=" N ARG G 259 " --> pdb=" O TYR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 305 removed outlier: 3.593A pdb=" N ILE G 303 " --> pdb=" O VAL G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 318 Processing helix chain 'G' and resid 324 through 328 Processing helix chain 'G' and resid 394 through 408 removed outlier: 3.533A pdb=" N GLN G 407 " --> pdb=" O LYS G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 427 removed outlier: 3.891A pdb=" N GLN G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 433 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'H' and resid 35 through 42 Processing helix chain 'H' and resid 56 through 65 Processing helix chain 'H' and resid 90 through 103 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'H' and resid 135 through 152 Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.346A pdb=" N GLN H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA H 178 " --> pdb=" O LEU H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 238 Processing helix chain 'H' and resid 247 through 253 removed outlier: 3.963A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 278 removed outlier: 4.301A pdb=" N ARG H 267 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU H 268 " --> pdb=" O PRO H 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 5.768A pdb=" N GLU A 85 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A 107 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE A 158 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N MET A 114 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 160 " --> pdb=" O MET A 114 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 116 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 157 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR A 198 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR A 159 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 217 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE A 268 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET A 219 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 85 removed outlier: 6.062A pdb=" N SER B 85 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 135 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLN B 107 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.274A pdb=" N ASN B 125 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 117 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 127 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 89 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.839A pdb=" N VAL C 31 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS C 4 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N HIS C 79 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 6 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AA7, first strand: chain 'C' and resid 222 through 229 removed outlier: 4.242A pdb=" N GLN C 213 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU C 227 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C 211 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 229 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS C 209 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 222 through 229 removed outlier: 4.242A pdb=" N GLN C 213 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU C 227 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C 211 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 229 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS C 209 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 234 removed outlier: 7.733A pdb=" N MET C 232 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 14.627A pdb=" N GLN C 237 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N ASN C 340 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 239 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 352 through 353 removed outlier: 3.516A pdb=" N GLY C 352 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AB3, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AB4, first strand: chain 'D' and resid 71 through 73 removed outlier: 4.583A pdb=" N VAL D 110 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 120 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE D 157 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 121 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N PHE D 159 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA D 123 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA D 161 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE D 125 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 156 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL D 197 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N CYS D 158 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR D 199 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER D 160 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU D 216 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 88 removed outlier: 5.732A pdb=" N GLU E 85 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 107 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ILE E 158 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET E 114 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE E 160 " --> pdb=" O MET E 114 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 116 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE E 157 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR E 198 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR E 159 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E 195 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASN E 218 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS E 197 " --> pdb=" O ASN E 218 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU E 220 " --> pdb=" O CYS E 197 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL E 217 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE E 268 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET E 219 " --> pdb=" O ILE E 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 202 through 204 Processing sheet with id=AB7, first strand: chain 'F' and resid 81 through 84 removed outlier: 4.027A pdb=" N VAL F 135 " --> pdb=" O GLN F 107 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN F 107 " --> pdb=" O VAL F 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 128 removed outlier: 3.710A pdb=" N CYS F 116 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 144 " --> pdb=" O PHE F 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 47 through 52 removed outlier: 6.610A pdb=" N THR G 28 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL G 49 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA G 30 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE G 51 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N HIS G 32 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL G 31 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS G 4 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS G 79 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL G 6 " --> pdb=" O HIS G 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 169 through 172 Processing sheet with id=AC2, first strand: chain 'G' and resid 222 through 227 removed outlier: 4.305A pdb=" N GLN G 213 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU G 227 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU G 211 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 214 " --> pdb=" O GLY G 273 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU G 288 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU G 278 " --> pdb=" O PHE G 286 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE G 286 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU G 280 " --> pdb=" O PHE G 284 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE G 284 " --> pdb=" O GLU G 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 229 through 234 removed outlier: 6.878A pdb=" N CYS G 230 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU G 241 " --> pdb=" O CYS G 230 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET G 232 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 14.645A pdb=" N GLN G 237 " --> pdb=" O ASN G 340 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N ASN G 340 " --> pdb=" O GLN G 237 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL G 239 " --> pdb=" O ARG G 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 352 through 353 removed outlier: 3.515A pdb=" N GLY G 352 " --> pdb=" O VAL G 377 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 357 through 358 Processing sheet with id=AC6, first strand: chain 'H' and resid 71 through 73 removed outlier: 4.418A pdb=" N VAL H 110 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER H 162 " --> pdb=" O THR H 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 218 through 219 828 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3242 1.32 - 1.45: 4104 1.45 - 1.57: 10197 1.57 - 1.70: 14 1.70 - 1.82: 218 Bond restraints: 17775 Sorted by residual: bond pdb=" N ASP F 130 " pdb=" CA ASP F 130 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.28e-02 6.10e+03 7.24e+00 bond pdb=" N GLY F 80 " pdb=" CA GLY F 80 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.35e+00 bond pdb=" N GLY B 80 " pdb=" CA GLY B 80 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.17e+00 bond pdb=" N LYS F 131 " pdb=" CA LYS F 131 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.83e+00 bond pdb=" N SER F 132 " pdb=" CA SER F 132 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.22e-02 6.72e+03 5.65e+00 ... (remaining 17770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 23673 1.87 - 3.74: 259 3.74 - 5.62: 45 5.62 - 7.49: 10 7.49 - 9.36: 6 Bond angle restraints: 23993 Sorted by residual: angle pdb=" CA GLY F 133 " pdb=" C GLY F 133 " pdb=" O GLY F 133 " ideal model delta sigma weight residual 121.75 118.25 3.50 1.02e+00 9.61e-01 1.18e+01 angle pdb=" C2' ADP G 501 " pdb=" C3' ADP G 501 " pdb=" C4' ADP G 501 " ideal model delta sigma weight residual 111.00 101.64 9.36 3.00e+00 1.11e-01 9.74e+00 angle pdb=" C2' ADP C 501 " pdb=" C3' ADP C 501 " pdb=" C4' ADP C 501 " ideal model delta sigma weight residual 111.00 101.69 9.31 3.00e+00 1.11e-01 9.62e+00 angle pdb=" N ASP F 130 " pdb=" CA ASP F 130 " pdb=" C ASP F 130 " ideal model delta sigma weight residual 113.88 110.17 3.71 1.23e+00 6.61e-01 9.10e+00 angle pdb=" CA ASP F 130 " pdb=" CB ASP F 130 " pdb=" CG ASP F 130 " ideal model delta sigma weight residual 112.60 115.51 -2.91 1.00e+00 1.00e+00 8.49e+00 ... (remaining 23988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 10682 28.71 - 57.42: 279 57.42 - 86.13: 35 86.13 - 114.84: 1 114.84 - 143.55: 4 Dihedral angle restraints: 11001 sinusoidal: 4596 harmonic: 6405 Sorted by residual: dihedral pdb=" O1B ADP G 501 " pdb=" O3A ADP G 501 " pdb=" PB ADP G 501 " pdb=" PA ADP G 501 " ideal model delta sinusoidal sigma weight residual 300.00 156.45 143.55 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 156.51 143.49 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP G 501 " pdb=" O5' ADP G 501 " pdb=" PA ADP G 501 " pdb=" O2A ADP G 501 " ideal model delta sinusoidal sigma weight residual -60.00 57.84 -117.84 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 10998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2239 0.053 - 0.106: 295 0.106 - 0.159: 123 0.159 - 0.211: 1 0.211 - 0.264: 2 Chirality restraints: 2660 Sorted by residual: chirality pdb=" CAP ACO D 302 " pdb=" C9P ACO D 302 " pdb=" CBP ACO D 302 " pdb=" OAP ACO D 302 " both_signs ideal model delta sigma weight residual False -2.31 -2.05 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CAP ACO H 302 " pdb=" C9P ACO H 302 " pdb=" CBP ACO H 302 " pdb=" OAP ACO H 302 " both_signs ideal model delta sigma weight residual False -2.31 -2.06 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C2' ADP C 501 " pdb=" C1' ADP C 501 " pdb=" C3' ADP C 501 " pdb=" O2' ADP C 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 2657 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 266 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C MET H 266 " -0.038 2.00e-02 2.50e+03 pdb=" O MET H 266 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG H 267 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 178 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ALA H 178 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA H 178 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS H 179 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP G 501 " -0.024 2.00e-02 2.50e+03 1.12e-02 3.47e+00 pdb=" C2 ADP G 501 " 0.006 2.00e-02 2.50e+03 pdb=" C4 ADP G 501 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP G 501 " 0.006 2.00e-02 2.50e+03 pdb=" C6 ADP G 501 " 0.000 2.00e-02 2.50e+03 pdb=" C8 ADP G 501 " 0.000 2.00e-02 2.50e+03 pdb=" N1 ADP G 501 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP G 501 " 0.008 2.00e-02 2.50e+03 pdb=" N6 ADP G 501 " -0.018 2.00e-02 2.50e+03 pdb=" N7 ADP G 501 " 0.014 2.00e-02 2.50e+03 pdb=" N9 ADP G 501 " 0.013 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 167 2.58 - 3.16: 14616 3.16 - 3.74: 26595 3.74 - 4.32: 38150 4.32 - 4.90: 65688 Nonbonded interactions: 145216 Sorted by model distance: nonbonded pdb=" O2A ADP C 501 " pdb="MG MG C 502 " model vdw 1.999 2.170 nonbonded pdb=" OE2 GLU C 288 " pdb="MG MG C 502 " model vdw 2.060 2.170 nonbonded pdb=" OH TYR A 140 " pdb=" O GLY A 207 " model vdw 2.197 3.040 nonbonded pdb=" O2A ADP G 501 " pdb="MG MG G 502 " model vdw 2.200 2.170 nonbonded pdb=" OG SER G 369 " pdb=" O ILE G 385 " model vdw 2.202 3.040 ... (remaining 145211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 23 through 302) selection = chain 'H' } 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=0.29 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: 5.220 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.040 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.004 0.070 17785 Z= 0.173 Angle : 0.560 9.361 24005 Z= 0.285 Chirality : 0.044 0.264 2660 Planarity : 0.004 0.036 3125 Dihedral : 13.156 143.545 6893 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 2228 helix: 0.98 (0.18), residues: 901 sheet: 0.04 (0.29), residues: 320 loop : -0.78 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 309 TYR 0.013 0.001 TYR H 35 PHE 0.011 0.001 PHE D 250 TRP 0.006 0.001 TRP A 61 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00377 (17775) covalent geometry : angle 0.55499 (23993) hydrogen bonds : bond 0.15616 ( 815) hydrogen bonds : angle 6.76592 ( 2352) metal coordination : bond 0.02713 ( 8) metal coordination : angle 3.46854 ( 12) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8019 (ptmt) cc_final: 0.7776 (mmtt) REVERT: A 122 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7770 (tpp-160) REVERT: A 154 LYS cc_start: 0.8395 (mptt) cc_final: 0.8145 (mmtp) REVERT: A 236 ILE cc_start: 0.8422 (mp) cc_final: 0.8012 (mp) REVERT: A 314 MET cc_start: 0.8241 (mmt) cc_final: 0.7993 (mmt) REVERT: B 85 SER cc_start: 0.8316 (t) cc_final: 0.8026 (t) REVERT: B 123 MET cc_start: 0.8007 (mtm) cc_final: 0.7733 (mtm) REVERT: B 149 ASP cc_start: 0.8222 (t0) cc_final: 0.7452 (t0) REVERT: C 58 LYS cc_start: 0.8456 (mttp) cc_final: 0.8115 (mmmt) REVERT: C 123 MET cc_start: 0.6026 (mmp) cc_final: 0.5418 (mmp) REVERT: C 142 MET cc_start: 0.5508 (mmm) cc_final: 0.5278 (tpt) REVERT: C 154 TYR cc_start: 0.6103 (m-80) cc_final: 0.5664 (m-80) REVERT: C 312 GLN cc_start: 0.8127 (mt0) cc_final: 0.7856 (mt0) REVERT: C 324 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7115 (mmmt) REVERT: C 407 GLN cc_start: 0.8538 (tt0) cc_final: 0.8235 (tt0) REVERT: D 118 MET cc_start: 0.7957 (ttp) cc_final: 0.7603 (mtm) REVERT: D 238 ARG cc_start: 0.8024 (ptp-110) cc_final: 0.7055 (mtt-85) REVERT: E 154 LYS cc_start: 0.8781 (mptt) cc_final: 0.8150 (mmmt) REVERT: E 183 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8134 (ttm170) REVERT: F 90 THR cc_start: 0.8087 (p) cc_final: 0.7815 (p) REVERT: F 93 ARG cc_start: 0.6764 (tpp80) cc_final: 0.6406 (tpp-160) REVERT: F 123 MET cc_start: 0.7365 (mtp) cc_final: 0.7134 (mtt) REVERT: G 203 TYR cc_start: 0.8100 (t80) cc_final: 0.7658 (t80) REVERT: G 204 LEU cc_start: 0.7382 (mt) cc_final: 0.6939 (mp) REVERT: G 206 ASN cc_start: 0.7937 (t0) cc_final: 0.7710 (m-40) REVERT: G 258 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6682 (tm-30) REVERT: G 324 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7607 (mtmm) REVERT: G 331 ARG cc_start: 0.8134 (ttt180) cc_final: 0.7836 (ttt90) REVERT: H 26 LYS cc_start: 0.7357 (mptt) cc_final: 0.6072 (ttpp) REVERT: H 41 ARG cc_start: 0.7644 (ptm-80) cc_final: 0.7436 (ptp-170) REVERT: H 44 GLU cc_start: 0.8456 (mp0) cc_final: 0.8139 (mm-30) REVERT: H 76 GLU cc_start: 0.7721 (mp0) cc_final: 0.7309 (pm20) REVERT: H 86 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.7100 (ttt90) REVERT: H 175 MET cc_start: 0.8252 (mmt) cc_final: 0.8034 (mmt) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.1867 time to fit residues: 108.0007 Evaluate side-chains 287 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 237 GLN C 290 ASN C 294 GLN E 65 GLN E 221 GLN F 126 GLN H 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121948 restraints weight = 19955.493| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.98 r_work: 0.3115 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17785 Z= 0.142 Angle : 0.569 8.881 24005 Z= 0.289 Chirality : 0.046 0.239 2660 Planarity : 0.004 0.044 3125 Dihedral : 8.788 118.160 2617 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.99 % Allowed : 6.32 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2228 helix: 1.48 (0.18), residues: 923 sheet: 0.27 (0.29), residues: 330 loop : -0.62 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 234 TYR 0.018 0.001 TYR C 203 PHE 0.027 0.002 PHE G 347 TRP 0.005 0.001 TRP E 238 HIS 0.008 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00327 (17775) covalent geometry : angle 0.56153 (23993) hydrogen bonds : bond 0.03929 ( 815) hydrogen bonds : angle 5.01149 ( 2352) metal coordination : bond 0.00565 ( 8) metal coordination : angle 4.02489 ( 12) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7967 (ptmt) cc_final: 0.7605 (mmtt) REVERT: A 154 LYS cc_start: 0.8426 (mptt) cc_final: 0.8194 (mmtt) REVERT: A 228 ILE cc_start: 0.8315 (tp) cc_final: 0.8085 (tt) REVERT: A 236 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 314 MET cc_start: 0.8268 (mmt) cc_final: 0.8021 (mmt) REVERT: B 149 ASP cc_start: 0.8213 (t0) cc_final: 0.7495 (t0) REVERT: C 58 LYS cc_start: 0.8496 (mttp) cc_final: 0.8200 (mmmt) REVERT: C 123 MET cc_start: 0.5140 (mmp) cc_final: 0.4906 (mmp) REVERT: C 142 MET cc_start: 0.5579 (mmm) cc_final: 0.5312 (tpt) REVERT: C 255 TYR cc_start: 0.6639 (t80) cc_final: 0.6388 (t80) REVERT: C 324 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7245 (mmmt) REVERT: C 437 ILE cc_start: 0.7882 (pt) cc_final: 0.7642 (mp) REVERT: D 118 MET cc_start: 0.8236 (ttp) cc_final: 0.7904 (mtm) REVERT: D 209 SER cc_start: 0.8294 (p) cc_final: 0.8073 (p) REVERT: E 154 LYS cc_start: 0.8723 (mptt) cc_final: 0.8199 (mmmt) REVERT: E 183 ARG cc_start: 0.8549 (ttm170) cc_final: 0.8329 (ttm110) REVERT: F 90 THR cc_start: 0.8062 (p) cc_final: 0.7759 (p) REVERT: F 93 ARG cc_start: 0.6702 (tpp80) cc_final: 0.6380 (mmt180) REVERT: G 96 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7777 (mm-30) REVERT: G 203 TYR cc_start: 0.8072 (t80) cc_final: 0.7586 (t80) REVERT: G 204 LEU cc_start: 0.7692 (mt) cc_final: 0.7208 (mp) REVERT: G 206 ASN cc_start: 0.8234 (t0) cc_final: 0.7911 (m-40) REVERT: G 234 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7791 (ttp-170) REVERT: G 258 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6825 (tm-30) REVERT: G 324 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7832 (mtpt) REVERT: G 331 ARG cc_start: 0.8294 (ttt180) cc_final: 0.7969 (ttt-90) REVERT: H 26 LYS cc_start: 0.7545 (mptt) cc_final: 0.6290 (ttpp) REVERT: H 44 GLU cc_start: 0.8397 (mp0) cc_final: 0.8161 (mm-30) REVERT: H 76 GLU cc_start: 0.7975 (mp0) cc_final: 0.7374 (pm20) outliers start: 18 outliers final: 10 residues processed: 302 average time/residue: 0.1719 time to fit residues: 74.4135 Evaluate side-chains 271 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 153 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 70 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 161 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS C 237 GLN C 438 HIS E 221 GLN H 42 ASN H 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119225 restraints weight = 20280.883| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.06 r_work: 0.3051 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17785 Z= 0.228 Angle : 0.607 7.960 24005 Z= 0.307 Chirality : 0.047 0.233 2660 Planarity : 0.005 0.050 3125 Dihedral : 8.609 115.943 2617 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.14 % Allowed : 7.80 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.18), residues: 2228 helix: 1.20 (0.18), residues: 941 sheet: 0.02 (0.29), residues: 306 loop : -0.75 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 235 TYR 0.023 0.002 TYR C 203 PHE 0.024 0.002 PHE G 347 TRP 0.009 0.002 TRP H 24 HIS 0.007 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00557 (17775) covalent geometry : angle 0.60025 (23993) hydrogen bonds : bond 0.04218 ( 815) hydrogen bonds : angle 4.88890 ( 2352) metal coordination : bond 0.00798 ( 8) metal coordination : angle 4.07047 ( 12) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7927 (ptmt) cc_final: 0.7632 (mmtt) REVERT: A 154 LYS cc_start: 0.8463 (mptt) cc_final: 0.8221 (mmtt) REVERT: A 236 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7978 (mp) REVERT: B 149 ASP cc_start: 0.8188 (t0) cc_final: 0.7385 (t0) REVERT: C 58 LYS cc_start: 0.8445 (mttp) cc_final: 0.8203 (mmmt) REVERT: C 123 MET cc_start: 0.5412 (mmp) cc_final: 0.5170 (mmp) REVERT: C 142 MET cc_start: 0.5498 (mmm) cc_final: 0.5149 (tpt) REVERT: C 255 TYR cc_start: 0.6784 (t80) cc_final: 0.6570 (t80) REVERT: C 324 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7263 (mmmt) REVERT: D 34 LEU cc_start: 0.9261 (mt) cc_final: 0.8908 (mt) REVERT: D 118 MET cc_start: 0.8210 (ttp) cc_final: 0.7851 (mtm) REVERT: E 126 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7282 (tt0) REVERT: E 154 LYS cc_start: 0.8730 (mptt) cc_final: 0.8201 (mmmt) REVERT: E 183 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8442 (ttm110) REVERT: F 90 THR cc_start: 0.8127 (p) cc_final: 0.7777 (p) REVERT: G 96 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 203 TYR cc_start: 0.8078 (t80) cc_final: 0.7567 (t80) REVERT: G 204 LEU cc_start: 0.7731 (mt) cc_final: 0.7209 (mp) REVERT: G 206 ASN cc_start: 0.8235 (t0) cc_final: 0.7904 (m-40) REVERT: G 234 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7910 (ttp-170) REVERT: G 324 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7974 (mtpt) REVERT: G 331 ARG cc_start: 0.8391 (ttt180) cc_final: 0.8066 (ttt-90) REVERT: H 26 LYS cc_start: 0.7601 (mptt) cc_final: 0.6320 (ttpp) REVERT: H 44 GLU cc_start: 0.8561 (mp0) cc_final: 0.8296 (mm-30) REVERT: H 76 GLU cc_start: 0.8119 (mp0) cc_final: 0.7433 (pm20) outliers start: 39 outliers final: 23 residues processed: 280 average time/residue: 0.1776 time to fit residues: 71.1346 Evaluate side-chains 278 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 44 optimal weight: 0.2980 chunk 186 optimal weight: 0.1980 chunk 110 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 194 optimal weight: 0.0030 chunk 201 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 189 optimal weight: 0.4980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN C 438 HIS E 118 HIS E 307 ASN H 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.163872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120794 restraints weight = 20159.477| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.04 r_work: 0.3111 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17785 Z= 0.108 Angle : 0.528 8.565 24005 Z= 0.265 Chirality : 0.044 0.230 2660 Planarity : 0.004 0.048 3125 Dihedral : 8.202 123.159 2617 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.54 % Allowed : 9.40 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2228 helix: 1.55 (0.18), residues: 931 sheet: 0.20 (0.30), residues: 306 loop : -0.69 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 235 TYR 0.020 0.001 TYR C 203 PHE 0.024 0.001 PHE G 347 TRP 0.005 0.001 TRP E 61 HIS 0.004 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00242 (17775) covalent geometry : angle 0.52037 (23993) hydrogen bonds : bond 0.03161 ( 815) hydrogen bonds : angle 4.54531 ( 2352) metal coordination : bond 0.00414 ( 8) metal coordination : angle 3.91114 ( 12) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7886 (ptmt) cc_final: 0.7631 (mmtt) REVERT: A 154 LYS cc_start: 0.8425 (mptt) cc_final: 0.8199 (mmtt) REVERT: A 236 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 149 ASP cc_start: 0.8185 (t0) cc_final: 0.7466 (t0) REVERT: C 58 LYS cc_start: 0.8486 (mttp) cc_final: 0.8280 (mmmt) REVERT: C 123 MET cc_start: 0.5448 (mmp) cc_final: 0.5178 (mmp) REVERT: C 142 MET cc_start: 0.5481 (mmm) cc_final: 0.5129 (tpt) REVERT: C 255 TYR cc_start: 0.6719 (t80) cc_final: 0.6429 (t80) REVERT: C 324 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7313 (mmmt) REVERT: C 350 SER cc_start: 0.8441 (t) cc_final: 0.8233 (p) REVERT: D 34 LEU cc_start: 0.9293 (mt) cc_final: 0.8869 (mt) REVERT: D 44 GLU cc_start: 0.8264 (mp0) cc_final: 0.7893 (mm-30) REVERT: D 118 MET cc_start: 0.8231 (ttp) cc_final: 0.7975 (mtm) REVERT: D 187 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8635 (ttp) REVERT: E 154 LYS cc_start: 0.8671 (mptt) cc_final: 0.8236 (mmpt) REVERT: E 183 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8349 (ttm110) REVERT: F 90 THR cc_start: 0.8186 (p) cc_final: 0.7851 (p) REVERT: G 96 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7829 (mm-30) REVERT: G 123 MET cc_start: 0.7546 (mmp) cc_final: 0.7288 (mmp) REVERT: G 203 TYR cc_start: 0.8088 (t80) cc_final: 0.7617 (t80) REVERT: G 204 LEU cc_start: 0.7832 (mt) cc_final: 0.7324 (mp) REVERT: G 206 ASN cc_start: 0.8178 (t0) cc_final: 0.7833 (m-40) REVERT: G 324 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7928 (mtpt) REVERT: G 331 ARG cc_start: 0.8296 (ttt180) cc_final: 0.7999 (ttt-90) REVERT: H 26 LYS cc_start: 0.7640 (mptt) cc_final: 0.6369 (ttpp) REVERT: H 41 ARG cc_start: 0.7780 (ptp-170) cc_final: 0.7539 (ptp-170) REVERT: H 76 GLU cc_start: 0.8134 (mp0) cc_final: 0.7443 (pm20) REVERT: H 80 LYS cc_start: 0.6514 (ttpp) cc_final: 0.6272 (tttt) REVERT: H 175 MET cc_start: 0.8519 (mmt) cc_final: 0.8201 (mmt) outliers start: 28 outliers final: 14 residues processed: 289 average time/residue: 0.1737 time to fit residues: 71.9744 Evaluate side-chains 279 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 192 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 64 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 185 optimal weight: 0.0980 chunk 171 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN E 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119879 restraints weight = 20207.730| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.02 r_work: 0.3103 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17785 Z= 0.129 Angle : 0.538 10.386 24005 Z= 0.268 Chirality : 0.044 0.241 2660 Planarity : 0.004 0.050 3125 Dihedral : 8.046 126.098 2617 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.87 % Allowed : 9.95 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.18), residues: 2228 helix: 1.56 (0.18), residues: 931 sheet: 0.22 (0.30), residues: 306 loop : -0.67 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 235 TYR 0.018 0.001 TYR C 154 PHE 0.023 0.001 PHE G 347 TRP 0.005 0.001 TRP E 61 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00304 (17775) covalent geometry : angle 0.53176 (23993) hydrogen bonds : bond 0.03208 ( 815) hydrogen bonds : angle 4.46533 ( 2352) metal coordination : bond 0.00489 ( 8) metal coordination : angle 3.68941 ( 12) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7878 (ptmt) cc_final: 0.7548 (mmtt) REVERT: A 154 LYS cc_start: 0.8415 (mptt) cc_final: 0.8188 (mmtt) REVERT: A 236 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8018 (mt) REVERT: B 149 ASP cc_start: 0.8098 (t0) cc_final: 0.7369 (t0) REVERT: C 58 LYS cc_start: 0.8450 (mttp) cc_final: 0.8229 (mmmt) REVERT: C 123 MET cc_start: 0.5695 (mmp) cc_final: 0.5247 (mmp) REVERT: C 142 MET cc_start: 0.5386 (mmm) cc_final: 0.5066 (tpt) REVERT: C 324 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7257 (mmmt) REVERT: C 350 SER cc_start: 0.8468 (t) cc_final: 0.8230 (p) REVERT: D 34 LEU cc_start: 0.9237 (mt) cc_final: 0.8883 (mt) REVERT: D 44 GLU cc_start: 0.8232 (mp0) cc_final: 0.7865 (mm-30) REVERT: D 118 MET cc_start: 0.8195 (ttp) cc_final: 0.7907 (mtm) REVERT: E 154 LYS cc_start: 0.8689 (mptt) cc_final: 0.8255 (mmpt) REVERT: E 183 ARG cc_start: 0.8623 (ttm170) cc_final: 0.8353 (ttm110) REVERT: F 90 THR cc_start: 0.7822 (p) cc_final: 0.7487 (p) REVERT: G 96 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7804 (mm-30) REVERT: G 203 TYR cc_start: 0.8082 (t80) cc_final: 0.7604 (t80) REVERT: G 204 LEU cc_start: 0.7791 (mt) cc_final: 0.7335 (mp) REVERT: G 206 ASN cc_start: 0.8177 (t0) cc_final: 0.7868 (m-40) REVERT: G 278 LEU cc_start: 0.8170 (mp) cc_final: 0.7880 (mm) REVERT: G 324 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7759 (mtpt) REVERT: G 331 ARG cc_start: 0.8299 (ttt180) cc_final: 0.7973 (ttt-90) REVERT: G 343 ASP cc_start: 0.7425 (t0) cc_final: 0.7082 (t0) REVERT: H 26 LYS cc_start: 0.7617 (mptt) cc_final: 0.6338 (ttpp) REVERT: H 41 ARG cc_start: 0.7735 (ptp-170) cc_final: 0.7421 (ptp-170) REVERT: H 76 GLU cc_start: 0.8147 (mp0) cc_final: 0.7441 (pm20) REVERT: H 80 LYS cc_start: 0.6360 (ttpp) cc_final: 0.6148 (tttt) REVERT: H 175 MET cc_start: 0.8498 (mmt) cc_final: 0.8168 (mmt) REVERT: H 203 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8249 (mtp) outliers start: 34 outliers final: 26 residues processed: 287 average time/residue: 0.1705 time to fit residues: 70.2934 Evaluate side-chains 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 203 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122304 restraints weight = 20099.460| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.00 r_work: 0.3104 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17785 Z= 0.128 Angle : 0.535 11.305 24005 Z= 0.266 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.924 129.602 2617 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.81 % Allowed : 10.44 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2228 helix: 1.60 (0.18), residues: 931 sheet: 0.25 (0.30), residues: 306 loop : -0.65 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 235 TYR 0.017 0.001 TYR C 203 PHE 0.024 0.001 PHE G 347 TRP 0.005 0.001 TRP H 24 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00303 (17775) covalent geometry : angle 0.52986 (23993) hydrogen bonds : bond 0.03135 ( 815) hydrogen bonds : angle 4.38078 ( 2352) metal coordination : bond 0.00454 ( 8) metal coordination : angle 3.43054 ( 12) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7860 (ptmt) cc_final: 0.7529 (mmtt) REVERT: A 236 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 149 ASP cc_start: 0.8076 (t0) cc_final: 0.7325 (t0) REVERT: C 123 MET cc_start: 0.5677 (mmp) cc_final: 0.5150 (mmp) REVERT: C 142 MET cc_start: 0.5422 (mmm) cc_final: 0.5175 (tpt) REVERT: C 200 MET cc_start: 0.7192 (tmm) cc_final: 0.6985 (ppp) REVERT: C 235 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8094 (mtm180) REVERT: C 324 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7328 (mmmt) REVERT: D 44 GLU cc_start: 0.8258 (mp0) cc_final: 0.7881 (mm-30) REVERT: D 118 MET cc_start: 0.8246 (ttp) cc_final: 0.7960 (mtm) REVERT: E 154 LYS cc_start: 0.8778 (mptt) cc_final: 0.8315 (mmpt) REVERT: E 183 ARG cc_start: 0.8636 (ttm170) cc_final: 0.8378 (ttm110) REVERT: F 90 THR cc_start: 0.7828 (p) cc_final: 0.7518 (p) REVERT: G 96 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7788 (mm-30) REVERT: G 203 TYR cc_start: 0.8103 (t80) cc_final: 0.7637 (t80) REVERT: G 204 LEU cc_start: 0.7914 (mt) cc_final: 0.7487 (mp) REVERT: G 206 ASN cc_start: 0.8177 (t0) cc_final: 0.7886 (m-40) REVERT: G 278 LEU cc_start: 0.8213 (mp) cc_final: 0.7969 (mm) REVERT: G 324 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7815 (mtpt) REVERT: G 331 ARG cc_start: 0.8277 (ttt180) cc_final: 0.7982 (ttt-90) REVERT: G 343 ASP cc_start: 0.7476 (t0) cc_final: 0.7143 (t0) REVERT: H 26 LYS cc_start: 0.7612 (mptt) cc_final: 0.6391 (ttpp) REVERT: H 41 ARG cc_start: 0.7792 (ptp-170) cc_final: 0.7480 (ptp-170) REVERT: H 76 GLU cc_start: 0.8215 (mp0) cc_final: 0.7600 (pm20) REVERT: H 80 LYS cc_start: 0.6399 (ttpp) cc_final: 0.6169 (tttt) REVERT: H 175 MET cc_start: 0.8519 (mmt) cc_final: 0.8222 (mmt) REVERT: H 203 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: H 278 MET cc_start: 0.8486 (mmm) cc_final: 0.8282 (mmm) outliers start: 33 outliers final: 25 residues processed: 286 average time/residue: 0.1573 time to fit residues: 64.7316 Evaluate side-chains 291 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 203 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 28 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 189 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN C 290 ASN C 294 GLN F 125 ASN H 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125814 restraints weight = 19809.322| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.02 r_work: 0.3094 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17785 Z= 0.162 Angle : 0.565 12.904 24005 Z= 0.280 Chirality : 0.045 0.233 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.912 130.923 2617 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.09 % Allowed : 11.21 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2228 helix: 1.50 (0.18), residues: 931 sheet: 0.07 (0.29), residues: 336 loop : -0.65 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 235 TYR 0.017 0.001 TYR C 203 PHE 0.024 0.001 PHE G 347 TRP 0.006 0.001 TRP H 24 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00393 (17775) covalent geometry : angle 0.55992 (23993) hydrogen bonds : bond 0.03378 ( 815) hydrogen bonds : angle 4.42916 ( 2352) metal coordination : bond 0.00579 ( 8) metal coordination : angle 3.35544 ( 12) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7509 (mmtt) REVERT: A 236 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8116 (mt) REVERT: B 124 MET cc_start: 0.8376 (mtm) cc_final: 0.7955 (mpt) REVERT: B 149 ASP cc_start: 0.8106 (t0) cc_final: 0.7381 (t0) REVERT: C 123 MET cc_start: 0.5731 (mmp) cc_final: 0.5300 (mmp) REVERT: C 142 MET cc_start: 0.5445 (mmm) cc_final: 0.5174 (tpt) REVERT: C 324 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7326 (mmmt) REVERT: D 34 LEU cc_start: 0.9244 (mt) cc_final: 0.8813 (mt) REVERT: D 44 GLU cc_start: 0.8232 (mp0) cc_final: 0.7863 (mm-30) REVERT: D 118 MET cc_start: 0.8141 (ttp) cc_final: 0.7877 (mtm) REVERT: E 126 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7273 (tt0) REVERT: E 154 LYS cc_start: 0.8858 (mptt) cc_final: 0.8340 (mmpt) REVERT: E 183 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8365 (ttm110) REVERT: F 90 THR cc_start: 0.7739 (p) cc_final: 0.7398 (p) REVERT: G 96 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7691 (mm-30) REVERT: G 203 TYR cc_start: 0.8112 (t80) cc_final: 0.7633 (t80) REVERT: G 204 LEU cc_start: 0.7872 (mt) cc_final: 0.7360 (mp) REVERT: G 206 ASN cc_start: 0.8176 (t0) cc_final: 0.7866 (m-40) REVERT: G 324 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7735 (mtpt) REVERT: G 331 ARG cc_start: 0.8303 (ttt180) cc_final: 0.8009 (ttt-90) REVERT: G 343 ASP cc_start: 0.7585 (t0) cc_final: 0.7290 (t0) REVERT: H 26 LYS cc_start: 0.7585 (mptt) cc_final: 0.6315 (ttpp) REVERT: H 41 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7510 (ptp-170) REVERT: H 76 GLU cc_start: 0.8229 (mp0) cc_final: 0.7619 (pm20) REVERT: H 175 MET cc_start: 0.8545 (mmt) cc_final: 0.8230 (mmt) REVERT: H 203 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: H 278 MET cc_start: 0.8444 (mmm) cc_final: 0.8194 (mtp) outliers start: 38 outliers final: 30 residues processed: 284 average time/residue: 0.1657 time to fit residues: 67.3071 Evaluate side-chains 292 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 203 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 195 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120195 restraints weight = 20225.168| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.17 r_work: 0.3089 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17785 Z= 0.137 Angle : 0.550 12.854 24005 Z= 0.272 Chirality : 0.045 0.233 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.847 131.623 2617 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2228 helix: 1.55 (0.18), residues: 927 sheet: 0.21 (0.29), residues: 314 loop : -0.63 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 235 TYR 0.016 0.001 TYR C 203 PHE 0.024 0.001 PHE G 347 TRP 0.006 0.001 TRP H 24 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00327 (17775) covalent geometry : angle 0.54446 (23993) hydrogen bonds : bond 0.03176 ( 815) hydrogen bonds : angle 4.38291 ( 2352) metal coordination : bond 0.00496 ( 8) metal coordination : angle 3.41424 ( 12) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 124 MET cc_start: 0.8367 (mtm) cc_final: 0.7929 (mpt) REVERT: B 149 ASP cc_start: 0.8100 (t0) cc_final: 0.7395 (t0) REVERT: C 123 MET cc_start: 0.5786 (mmp) cc_final: 0.5215 (mmp) REVERT: C 142 MET cc_start: 0.5341 (mmm) cc_final: 0.5117 (tpt) REVERT: C 324 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7334 (mmmt) REVERT: D 34 LEU cc_start: 0.9296 (mt) cc_final: 0.8891 (mt) REVERT: D 44 GLU cc_start: 0.8254 (mp0) cc_final: 0.7887 (mm-30) REVERT: D 118 MET cc_start: 0.8149 (ttp) cc_final: 0.7899 (mtm) REVERT: E 126 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7301 (tt0) REVERT: E 154 LYS cc_start: 0.8850 (mptt) cc_final: 0.8342 (mmpt) REVERT: E 183 ARG cc_start: 0.8659 (ttm170) cc_final: 0.8398 (ttm110) REVERT: E 251 MET cc_start: 0.8113 (mtt) cc_final: 0.7896 (mtt) REVERT: F 90 THR cc_start: 0.7754 (p) cc_final: 0.7419 (p) REVERT: G 96 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7703 (mm-30) REVERT: G 203 TYR cc_start: 0.8069 (t80) cc_final: 0.7585 (t80) REVERT: G 204 LEU cc_start: 0.7899 (mt) cc_final: 0.7365 (mp) REVERT: G 206 ASN cc_start: 0.8191 (t0) cc_final: 0.7879 (m-40) REVERT: G 278 LEU cc_start: 0.8280 (mp) cc_final: 0.7992 (mm) REVERT: G 324 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7725 (mtpt) REVERT: G 331 ARG cc_start: 0.8291 (ttt180) cc_final: 0.7991 (ttt-90) REVERT: G 343 ASP cc_start: 0.7612 (t0) cc_final: 0.7326 (t0) REVERT: H 26 LYS cc_start: 0.7623 (mptt) cc_final: 0.6400 (ttpp) REVERT: H 41 ARG cc_start: 0.7996 (ptp-170) cc_final: 0.7582 (ptp-170) REVERT: H 76 GLU cc_start: 0.8237 (mp0) cc_final: 0.7622 (pm20) REVERT: H 175 MET cc_start: 0.8551 (mmt) cc_final: 0.8243 (mmt) REVERT: H 203 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: H 278 MET cc_start: 0.8416 (mmm) cc_final: 0.8167 (mtp) outliers start: 35 outliers final: 28 residues processed: 282 average time/residue: 0.1635 time to fit residues: 66.3140 Evaluate side-chains 289 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 203 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 76 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN H 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120277 restraints weight = 20287.082| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.00 r_work: 0.3136 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17785 Z= 0.134 Angle : 0.547 13.335 24005 Z= 0.271 Chirality : 0.045 0.233 2660 Planarity : 0.004 0.051 3125 Dihedral : 7.797 132.794 2617 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 11.59 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2228 helix: 1.57 (0.18), residues: 927 sheet: 0.11 (0.29), residues: 334 loop : -0.60 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 235 TYR 0.016 0.001 TYR C 203 PHE 0.025 0.001 PHE G 347 TRP 0.005 0.001 TRP H 24 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00319 (17775) covalent geometry : angle 0.54228 (23993) hydrogen bonds : bond 0.03154 ( 815) hydrogen bonds : angle 4.36277 ( 2352) metal coordination : bond 0.00469 ( 8) metal coordination : angle 3.36161 ( 12) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 124 MET cc_start: 0.8358 (mtm) cc_final: 0.7912 (mpt) REVERT: B 149 ASP cc_start: 0.8145 (t0) cc_final: 0.7431 (t0) REVERT: C 123 MET cc_start: 0.5854 (mmp) cc_final: 0.5291 (mmp) REVERT: C 142 MET cc_start: 0.5308 (mmm) cc_final: 0.5096 (tpt) REVERT: C 324 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7425 (mmmt) REVERT: D 34 LEU cc_start: 0.9361 (mt) cc_final: 0.8979 (mt) REVERT: D 44 GLU cc_start: 0.8284 (mp0) cc_final: 0.7901 (mm-30) REVERT: D 118 MET cc_start: 0.8165 (ttp) cc_final: 0.7949 (mtm) REVERT: E 126 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7386 (tt0) REVERT: E 154 LYS cc_start: 0.8887 (mptt) cc_final: 0.8395 (mmpt) REVERT: E 183 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8419 (ttm110) REVERT: F 90 THR cc_start: 0.7841 (p) cc_final: 0.7514 (p) REVERT: G 96 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7678 (mm-30) REVERT: G 203 TYR cc_start: 0.8110 (t80) cc_final: 0.7653 (t80) REVERT: G 204 LEU cc_start: 0.8032 (mt) cc_final: 0.7535 (mp) REVERT: G 206 ASN cc_start: 0.8173 (t0) cc_final: 0.7896 (m-40) REVERT: G 278 LEU cc_start: 0.8359 (mp) cc_final: 0.8053 (mm) REVERT: G 324 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7851 (mtpt) REVERT: G 331 ARG cc_start: 0.8235 (ttt180) cc_final: 0.8015 (ttt-90) REVERT: G 343 ASP cc_start: 0.7619 (t0) cc_final: 0.7349 (t0) REVERT: H 26 LYS cc_start: 0.7655 (mptt) cc_final: 0.6472 (ttpp) REVERT: H 41 ARG cc_start: 0.8029 (ptp-170) cc_final: 0.7608 (ptp-170) REVERT: H 73 LEU cc_start: 0.8350 (mt) cc_final: 0.8143 (mp) REVERT: H 76 GLU cc_start: 0.8274 (mp0) cc_final: 0.7668 (pm20) REVERT: H 175 MET cc_start: 0.8560 (mmt) cc_final: 0.8287 (mmt) REVERT: H 203 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8147 (mtp) outliers start: 36 outliers final: 31 residues processed: 282 average time/residue: 0.1609 time to fit residues: 65.1898 Evaluate side-chains 293 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 203 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 78 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122499 restraints weight = 19972.065| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.98 r_work: 0.3150 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17785 Z= 0.130 Angle : 0.551 13.569 24005 Z= 0.273 Chirality : 0.045 0.233 2660 Planarity : 0.004 0.051 3125 Dihedral : 7.764 132.729 2617 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.81 % Allowed : 11.81 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2228 helix: 1.55 (0.18), residues: 927 sheet: 0.14 (0.29), residues: 334 loop : -0.60 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 235 TYR 0.016 0.001 TYR C 203 PHE 0.025 0.001 PHE G 347 TRP 0.005 0.001 TRP H 24 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00309 (17775) covalent geometry : angle 0.54588 (23993) hydrogen bonds : bond 0.03136 ( 815) hydrogen bonds : angle 4.37314 ( 2352) metal coordination : bond 0.00452 ( 8) metal coordination : angle 3.32029 ( 12) Misc. bond : bond 0.00025 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8157 (mt) REVERT: B 124 MET cc_start: 0.8336 (mtm) cc_final: 0.7914 (mpt) REVERT: B 149 ASP cc_start: 0.8139 (t0) cc_final: 0.7427 (t0) REVERT: C 123 MET cc_start: 0.5849 (mmp) cc_final: 0.5294 (mmp) REVERT: C 142 MET cc_start: 0.5321 (mmm) cc_final: 0.5102 (tpt) REVERT: C 324 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7417 (mmmt) REVERT: D 34 LEU cc_start: 0.9357 (mt) cc_final: 0.8981 (mt) REVERT: D 36 ARG cc_start: 0.8337 (tpp80) cc_final: 0.8131 (tpp80) REVERT: D 44 GLU cc_start: 0.8264 (mp0) cc_final: 0.7894 (mm-30) REVERT: D 111 MET cc_start: 0.8576 (mtp) cc_final: 0.8360 (mtp) REVERT: E 154 LYS cc_start: 0.8868 (mptt) cc_final: 0.8376 (mmpt) REVERT: E 183 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8413 (ttm110) REVERT: E 282 MET cc_start: 0.7840 (tpp) cc_final: 0.7176 (tpt) REVERT: F 90 THR cc_start: 0.7818 (p) cc_final: 0.7493 (p) REVERT: G 96 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7747 (mm-30) REVERT: G 203 TYR cc_start: 0.8136 (t80) cc_final: 0.7685 (t80) REVERT: G 204 LEU cc_start: 0.8013 (mt) cc_final: 0.7516 (mp) REVERT: G 206 ASN cc_start: 0.8161 (t0) cc_final: 0.7886 (m-40) REVERT: G 278 LEU cc_start: 0.8335 (mp) cc_final: 0.8036 (mm) REVERT: G 324 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7814 (mtpt) REVERT: G 331 ARG cc_start: 0.8268 (ttt180) cc_final: 0.8046 (ttt-90) REVERT: G 343 ASP cc_start: 0.7618 (t0) cc_final: 0.7344 (t0) REVERT: H 26 LYS cc_start: 0.7640 (mptt) cc_final: 0.6457 (ttpp) REVERT: H 41 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7569 (ptp-170) REVERT: H 76 GLU cc_start: 0.8329 (mp0) cc_final: 0.7695 (pm20) REVERT: H 175 MET cc_start: 0.8547 (mmt) cc_final: 0.8275 (mmt) REVERT: H 203 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8133 (mtp) outliers start: 33 outliers final: 27 residues processed: 279 average time/residue: 0.1615 time to fit residues: 64.6483 Evaluate side-chains 293 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 203 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 198 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125190 restraints weight = 20136.909| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.98 r_work: 0.3179 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17785 Z= 0.104 Angle : 0.536 13.616 24005 Z= 0.263 Chirality : 0.044 0.233 2660 Planarity : 0.004 0.051 3125 Dihedral : 7.618 132.691 2617 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.59 % Allowed : 12.47 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2228 helix: 1.69 (0.18), residues: 924 sheet: -0.04 (0.28), residues: 362 loop : -0.48 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 235 TYR 0.014 0.001 TYR C 203 PHE 0.025 0.001 PHE G 347 TRP 0.005 0.001 TRP E 61 HIS 0.004 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00240 (17775) covalent geometry : angle 0.53113 (23993) hydrogen bonds : bond 0.02847 ( 815) hydrogen bonds : angle 4.26040 ( 2352) metal coordination : bond 0.00352 ( 8) metal coordination : angle 3.18205 ( 12) Misc. bond : bond 0.00017 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5688.00 seconds wall clock time: 98 minutes 5.09 seconds (5885.09 seconds total)