Starting phenix.real_space_refine on Sun Jun 15 15:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uz2_42831/06_2025/8uz2_42831_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uz2_42831/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uz2_42831/06_2025/8uz2_42831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uz2_42831/06_2025/8uz2_42831.map" model { file = "/net/cci-nas-00/data/ceres_data/8uz2_42831/06_2025/8uz2_42831_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uz2_42831/06_2025/8uz2_42831_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.87, per 1000 atoms: 0.68 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: 4.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.37 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: 5.94 Time building geometry restraints manager: 5.32 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 285 or resid 301 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: 6.880 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 46.570 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.006 0.001 TRP A 61 HIS 0.005 0.001 HIS E 118 PHE 0.011 0.001 PHE D 250 TYR 0.013 0.001 TYR H 35 ARG 0.007 0.001 ARG E 309 Details of bonding type rmsd hydrogen bonds : bond 0.15616 ( 815) hydrogen bonds : angle 6.76592 ( 2352) metal coordination : bond 0.02713 ( 8) metal coordination : angle 3.46854 ( 12) covalent geometry : bond 0.00377 (17775) covalent geometry : angle 0.55499 (23993) 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 : 1.954 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: 0.8027 (t) REVERT: B 123 MET cc_start: 0.8007 (mtm) cc_final: 0.7732 (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: 0.8116 (mmmt) REVERT: C 123 MET cc_start: 0.6026 (mmp) cc_final: 0.5417 (mmp) REVERT: C 154 TYR cc_start: 0.6103 (m-80) cc_final: 0.5664 (m-80) REVERT: C 296 GLU cc_start: 0.8813 (pm20) cc_final: 0.8562 (pm20) REVERT: C 312 GLN cc_start: 0.8127 (mt0) cc_final: 0.7854 (mt0) REVERT: C 324 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7114 (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: 0.7602 (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: 0.8149 (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: 0.6407 (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 175 MET cc_start: 0.8252 (mmt) cc_final: 0.8034 (mmt) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.3742 time to fit residues: 215.5997 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 : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117769 restraints weight = 20109.832| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.00 r_work: 0.3081 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17785 Z= 0.196 Angle : 0.602 9.067 24005 Z= 0.307 Chirality : 0.047 0.241 2660 Planarity : 0.005 0.055 3125 Dihedral : 8.869 118.148 2617 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.15 % Allowed : 6.59 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2228 helix: 1.37 (0.18), residues: 919 sheet: 0.31 (0.29), residues: 308 loop : -0.78 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 238 HIS 0.010 0.002 HIS E 69 PHE 0.029 0.002 PHE G 347 TYR 0.019 0.002 TYR C 203 ARG 0.007 0.001 ARG G 234 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 815) hydrogen bonds : angle 5.11090 ( 2352) metal coordination : bond 0.00692 ( 8) metal coordination : angle 4.13637 ( 12) covalent geometry : bond 0.00466 (17775) covalent geometry : angle 0.59455 (23993) Misc. bond : bond 0.00054 ( 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 304 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7972 (ptmt) cc_final: 0.7630 (mmtt) REVERT: A 154 LYS cc_start: 0.8426 (mptt) cc_final: 0.8183 (mmtt) REVERT: A 228 ILE cc_start: 0.8417 (tp) cc_final: 0.8199 (tt) REVERT: A 236 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 314 MET cc_start: 0.8334 (mmt) cc_final: 0.8120 (mmt) REVERT: B 104 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7464 (tm-30) REVERT: B 149 ASP cc_start: 0.8296 (t0) cc_final: 0.7561 (t0) REVERT: C 58 LYS cc_start: 0.8454 (mttp) cc_final: 0.8182 (mmmt) REVERT: C 97 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8478 (mmm160) REVERT: C 123 MET cc_start: 0.5411 (mmp) cc_final: 0.5157 (mmp) REVERT: C 255 TYR cc_start: 0.6721 (t80) cc_final: 0.6472 (t80) REVERT: C 324 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7260 (mmmt) REVERT: D 40 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7765 (mt-10) REVERT: D 118 MET cc_start: 0.8183 (ttp) cc_final: 0.7858 (mtm) REVERT: E 126 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7205 (tt0) REVERT: E 154 LYS cc_start: 0.8698 (mptt) cc_final: 0.8174 (mmmt) REVERT: E 183 ARG cc_start: 0.8614 (ttm170) cc_final: 0.8402 (ttm110) REVERT: E 219 MET cc_start: 0.8523 (ttm) cc_final: 0.8173 (ttp) REVERT: F 90 THR cc_start: 0.8143 (p) cc_final: 0.7816 (p) REVERT: F 93 ARG cc_start: 0.6768 (tpp80) cc_final: 0.6421 (mmt180) REVERT: F 123 MET cc_start: 0.7287 (mtp) cc_final: 0.7055 (mtt) REVERT: G 96 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7756 (mm-30) REVERT: G 203 TYR cc_start: 0.8088 (t80) cc_final: 0.7594 (t80) REVERT: G 204 LEU cc_start: 0.7702 (mt) cc_final: 0.7196 (mp) REVERT: G 206 ASN cc_start: 0.8228 (t0) cc_final: 0.7902 (m-40) REVERT: G 234 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7819 (ttp-170) REVERT: G 258 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6846 (tm-30) REVERT: G 324 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7934 (mtpt) REVERT: G 331 ARG cc_start: 0.8342 (ttt180) cc_final: 0.8024 (ttt-90) REVERT: H 26 LYS cc_start: 0.7576 (mptt) cc_final: 0.6272 (ttpp) REVERT: H 44 GLU cc_start: 0.8503 (mp0) cc_final: 0.8266 (mm-30) REVERT: H 76 GLU cc_start: 0.8042 (mp0) cc_final: 0.7395 (pm20) outliers start: 21 outliers final: 13 residues processed: 295 average time/residue: 0.3473 time to fit residues: 146.8826 Evaluate side-chains 276 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 135 ASP 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 E residue 266 SER Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 5 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 191 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 218 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 65 GLN E 118 HIS H 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126775 restraints weight = 19712.906| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.09 r_work: 0.3082 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17785 Z= 0.147 Angle : 0.552 8.473 24005 Z= 0.279 Chirality : 0.045 0.230 2660 Planarity : 0.004 0.048 3125 Dihedral : 8.516 118.514 2617 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.59 % Allowed : 8.30 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2228 helix: 1.47 (0.18), residues: 931 sheet: 0.08 (0.29), residues: 306 loop : -0.72 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 24 HIS 0.006 0.001 HIS E 69 PHE 0.024 0.001 PHE G 347 TYR 0.022 0.002 TYR G 439 ARG 0.005 0.000 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 815) hydrogen bonds : angle 4.74190 ( 2352) metal coordination : bond 0.00571 ( 8) metal coordination : angle 4.00453 ( 12) covalent geometry : bond 0.00347 (17775) covalent geometry : angle 0.54488 (23993) Misc. bond : bond 0.00045 ( 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 303 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7897 (ptmt) cc_final: 0.7620 (mmtt) REVERT: A 154 LYS cc_start: 0.8425 (mptt) cc_final: 0.8197 (mmtt) REVERT: A 236 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 314 MET cc_start: 0.8294 (mmt) cc_final: 0.8030 (mmt) REVERT: B 149 ASP cc_start: 0.8137 (t0) cc_final: 0.7344 (t0) REVERT: C 58 LYS cc_start: 0.8476 (mttp) cc_final: 0.8246 (mmmt) REVERT: C 123 MET cc_start: 0.5366 (mmp) cc_final: 0.5151 (mmp) REVERT: C 142 MET cc_start: 0.5017 (tpt) cc_final: 0.4697 (mmm) REVERT: C 200 MET cc_start: 0.7457 (ppp) cc_final: 0.6737 (ppp) REVERT: C 255 TYR cc_start: 0.6721 (t80) cc_final: 0.6489 (t80) REVERT: C 324 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7302 (mmmt) REVERT: D 34 LEU cc_start: 0.9287 (mt) cc_final: 0.8944 (mt) REVERT: D 40 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7816 (mt-10) REVERT: D 44 GLU cc_start: 0.8225 (mp0) cc_final: 0.7863 (mm-30) REVERT: D 118 MET cc_start: 0.8166 (ttp) cc_final: 0.7882 (mtm) REVERT: E 154 LYS cc_start: 0.8693 (mptt) cc_final: 0.8205 (mmmt) REVERT: E 183 ARG cc_start: 0.8600 (ttm170) cc_final: 0.8362 (ttm110) REVERT: F 90 THR cc_start: 0.8108 (p) cc_final: 0.7767 (p) REVERT: G 96 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7815 (mm-30) REVERT: G 203 TYR cc_start: 0.8094 (t80) cc_final: 0.7599 (t80) REVERT: G 204 LEU cc_start: 0.7754 (mt) cc_final: 0.7246 (mp) REVERT: G 206 ASN cc_start: 0.8240 (t0) cc_final: 0.7930 (m-40) REVERT: G 234 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7967 (ttp-170) REVERT: G 324 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8005 (mtpt) REVERT: G 331 ARG cc_start: 0.8308 (ttt180) cc_final: 0.7997 (ttt-90) REVERT: H 26 LYS cc_start: 0.7624 (mptt) cc_final: 0.6323 (ttpp) REVERT: H 76 GLU cc_start: 0.8103 (mp0) cc_final: 0.7431 (pm20) outliers start: 29 outliers final: 15 residues processed: 287 average time/residue: 0.3361 time to fit residues: 139.2612 Evaluate side-chains 273 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 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 E residue 6 LEU 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 G residue 38 ASP Chi-restraints excluded: chain G residue 265 VAL 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 7 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 290 ASN C 294 GLN C 438 HIS ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120366 restraints weight = 20209.969| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.26 r_work: 0.3176 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17785 Z= 0.260 Angle : 0.632 8.649 24005 Z= 0.319 Chirality : 0.048 0.231 2660 Planarity : 0.005 0.052 3125 Dihedral : 8.558 122.499 2617 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.25 % Allowed : 9.45 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2228 helix: 1.02 (0.17), residues: 942 sheet: -0.13 (0.28), residues: 316 loop : -0.89 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 24 HIS 0.007 0.001 HIS E 69 PHE 0.022 0.002 PHE G 347 TYR 0.021 0.002 TYR E 225 ARG 0.006 0.001 ARG E 122 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 815) hydrogen bonds : angle 4.82544 ( 2352) metal coordination : bond 0.00887 ( 8) metal coordination : angle 4.04550 ( 12) covalent geometry : bond 0.00638 (17775) covalent geometry : angle 0.62575 (23993) Misc. bond : bond 0.00078 ( 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 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7969 (ptmt) cc_final: 0.7677 (mmtt) REVERT: A 154 LYS cc_start: 0.8367 (mptt) cc_final: 0.8122 (mmtt) REVERT: A 236 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8225 (mt) REVERT: B 149 ASP cc_start: 0.8137 (t0) cc_final: 0.7376 (t0) REVERT: C 58 LYS cc_start: 0.8454 (mttp) cc_final: 0.8223 (mmmt) REVERT: C 123 MET cc_start: 0.5766 (mmp) cc_final: 0.5276 (mmp) REVERT: C 200 MET cc_start: 0.7515 (ppp) cc_final: 0.6865 (ppp) REVERT: C 255 TYR cc_start: 0.6668 (t80) cc_final: 0.6325 (t80) REVERT: C 324 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7164 (mmmt) REVERT: D 34 LEU cc_start: 0.9209 (mt) cc_final: 0.8869 (mt) REVERT: D 40 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7755 (mt-10) REVERT: D 44 GLU cc_start: 0.8240 (mp0) cc_final: 0.7748 (mm-30) REVERT: D 118 MET cc_start: 0.8237 (ttp) cc_final: 0.7787 (mtm) REVERT: E 126 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7113 (tt0) REVERT: E 154 LYS cc_start: 0.8769 (mptt) cc_final: 0.8239 (mmpt) REVERT: F 90 THR cc_start: 0.7859 (p) cc_final: 0.7483 (p) REVERT: F 102 PHE cc_start: 0.8189 (m-10) cc_final: 0.7942 (m-10) REVERT: G 96 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7783 (mm-30) REVERT: G 123 MET cc_start: 0.7392 (mmp) cc_final: 0.7173 (mmp) REVERT: G 203 TYR cc_start: 0.8015 (t80) cc_final: 0.7547 (t80) REVERT: G 204 LEU cc_start: 0.7719 (mt) cc_final: 0.7151 (mp) REVERT: G 206 ASN cc_start: 0.8242 (t0) cc_final: 0.7879 (m-40) REVERT: G 234 ARG cc_start: 0.8256 (ttp80) cc_final: 0.8002 (ttp-170) REVERT: G 324 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7788 (mtpt) REVERT: G 331 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8085 (ttt-90) REVERT: H 26 LYS cc_start: 0.7574 (mptt) cc_final: 0.6167 (ttpp) REVERT: H 41 ARG cc_start: 0.7816 (ptp-110) cc_final: 0.7386 (ptp-170) REVERT: H 73 LEU cc_start: 0.8175 (mt) cc_final: 0.7899 (mp) REVERT: H 76 GLU cc_start: 0.8205 (mp0) cc_final: 0.7434 (pm20) outliers start: 41 outliers final: 29 residues processed: 281 average time/residue: 0.3730 time to fit residues: 152.6073 Evaluate side-chains 283 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 B residue 88 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 393 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 192 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 163 THR 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 109 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 15 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 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 131 optimal weight: 0.5980 chunk 156 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 307 ASN F 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.166775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126306 restraints weight = 19968.214| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.08 r_work: 0.3091 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| |-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: 0.8054 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17785 Z= 0.136 Angle : 0.552 9.725 24005 Z= 0.276 Chirality : 0.045 0.233 2660 Planarity : 0.004 0.051 3125 Dihedral : 8.297 131.265 2617 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.70 % Allowed : 10.38 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2228 helix: 1.33 (0.18), residues: 933 sheet: -0.06 (0.29), residues: 304 loop : -0.78 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 61 HIS 0.005 0.001 HIS E 69 PHE 0.024 0.001 PHE G 347 TYR 0.021 0.001 TYR C 154 ARG 0.004 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 815) hydrogen bonds : angle 4.58447 ( 2352) metal coordination : bond 0.00527 ( 8) metal coordination : angle 4.09490 ( 12) covalent geometry : bond 0.00323 (17775) covalent geometry : angle 0.54445 (23993) Misc. bond : bond 0.00034 ( 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 301 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7894 (ptmt) cc_final: 0.7623 (mmtt) REVERT: A 236 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 149 ASP cc_start: 0.8080 (t0) cc_final: 0.7337 (t0) REVERT: C 58 LYS cc_start: 0.8428 (mttp) cc_final: 0.8213 (mmmt) REVERT: C 123 MET cc_start: 0.5700 (mmp) cc_final: 0.5240 (mmp) REVERT: C 142 MET cc_start: 0.4964 (tpt) cc_final: 0.4669 (mmm) REVERT: C 200 MET cc_start: 0.7484 (ppp) cc_final: 0.6826 (ppp) REVERT: C 324 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7339 (mmmt) REVERT: D 34 LEU cc_start: 0.9281 (mt) cc_final: 0.8937 (mt) REVERT: D 40 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7698 (mt-10) REVERT: D 44 GLU cc_start: 0.8230 (mp0) cc_final: 0.7860 (mm-30) REVERT: D 118 MET cc_start: 0.8112 (ttp) cc_final: 0.7849 (mtm) REVERT: E 154 LYS cc_start: 0.8834 (mptt) cc_final: 0.8317 (mmpt) REVERT: E 219 MET cc_start: 0.8732 (ttm) cc_final: 0.8351 (ttt) REVERT: E 266 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8590 (p) REVERT: F 90 THR cc_start: 0.7808 (p) cc_final: 0.7427 (p) REVERT: G 96 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7720 (mm-30) REVERT: G 203 TYR cc_start: 0.8069 (t80) cc_final: 0.7573 (t80) REVERT: G 204 LEU cc_start: 0.7822 (mt) cc_final: 0.7293 (mp) REVERT: G 206 ASN cc_start: 0.8147 (t0) cc_final: 0.7813 (m-40) REVERT: G 324 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7901 (mtpt) REVERT: G 331 ARG cc_start: 0.8303 (ttt180) cc_final: 0.8017 (ttt-90) REVERT: G 343 ASP cc_start: 0.7599 (t0) cc_final: 0.7359 (t0) REVERT: H 26 LYS cc_start: 0.7594 (mptt) cc_final: 0.6362 (ttpp) REVERT: H 41 ARG cc_start: 0.7869 (ptp-110) cc_final: 0.7412 (ptp-170) REVERT: H 76 GLU cc_start: 0.8209 (mp0) cc_final: 0.7516 (pm20) outliers start: 31 outliers final: 20 residues processed: 287 average time/residue: 0.4031 time to fit residues: 167.4836 Evaluate side-chains 282 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain C residue 264 CYS 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 192 LEU Chi-restraints excluded: chain D residue 235 GLN 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 266 SER 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 H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 0.0030 chunk 67 optimal weight: 0.3980 chunk 182 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 198 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 overall best weight: 0.2286 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.165237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123757 restraints weight = 20071.559| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.13 r_work: 0.3143 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17785 Z= 0.101 Angle : 0.526 10.090 24005 Z= 0.262 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.941 136.850 2617 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.37 % Allowed : 11.48 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2228 helix: 1.56 (0.18), residues: 932 sheet: 0.14 (0.30), residues: 304 loop : -0.67 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 61 HIS 0.004 0.001 HIS E 69 PHE 0.024 0.001 PHE G 347 TYR 0.013 0.001 TYR G 439 ARG 0.005 0.000 ARG E 183 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 815) hydrogen bonds : angle 4.36028 ( 2352) metal coordination : bond 0.00361 ( 8) metal coordination : angle 3.96687 ( 12) covalent geometry : bond 0.00225 (17775) covalent geometry : angle 0.51886 (23993) Misc. bond : bond 0.00020 ( 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: 25 poor density : 279 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7842 (ptmt) cc_final: 0.7501 (mmtt) REVERT: A 236 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8124 (mt) REVERT: B 149 ASP cc_start: 0.8119 (t0) cc_final: 0.7399 (t0) REVERT: C 58 LYS cc_start: 0.8506 (mttp) cc_final: 0.8266 (mmmt) REVERT: C 123 MET cc_start: 0.5668 (mmp) cc_final: 0.5138 (mmp) REVERT: C 142 MET cc_start: 0.5107 (tpt) cc_final: 0.4890 (mmm) REVERT: C 200 MET cc_start: 0.7313 (ppp) cc_final: 0.6783 (ppp) REVERT: C 255 TYR cc_start: 0.6431 (t80) cc_final: 0.6229 (t80) REVERT: C 324 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7291 (mmmt) REVERT: D 34 LEU cc_start: 0.9296 (mt) cc_final: 0.8895 (mt) REVERT: D 44 GLU cc_start: 0.8214 (mp0) cc_final: 0.7913 (mm-30) REVERT: D 118 MET cc_start: 0.8131 (ttp) cc_final: 0.7886 (mtm) REVERT: D 187 MET cc_start: 0.8697 (ttm) cc_final: 0.8233 (ttt) REVERT: E 154 LYS cc_start: 0.8840 (mptt) cc_final: 0.8274 (mmmt) REVERT: E 183 ARG cc_start: 0.8651 (ttm110) cc_final: 0.8362 (ttm110) REVERT: E 219 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8284 (ttt) REVERT: F 90 THR cc_start: 0.7720 (p) cc_final: 0.7376 (p) REVERT: G 96 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7829 (mm-30) REVERT: G 203 TYR cc_start: 0.8078 (t80) cc_final: 0.7607 (t80) REVERT: G 204 LEU cc_start: 0.7842 (mt) cc_final: 0.7322 (mp) REVERT: G 206 ASN cc_start: 0.8135 (t0) cc_final: 0.7783 (m-40) REVERT: G 324 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7743 (mtpt) REVERT: G 331 ARG cc_start: 0.8304 (ttt180) cc_final: 0.8008 (ttt-90) REVERT: G 343 ASP cc_start: 0.7546 (t0) cc_final: 0.7256 (t0) REVERT: H 26 LYS cc_start: 0.7605 (mptt) cc_final: 0.6360 (ttpp) REVERT: H 41 ARG cc_start: 0.7840 (ptp-110) cc_final: 0.7390 (ptp-170) REVERT: H 76 GLU cc_start: 0.8238 (mp0) cc_final: 0.7541 (pm20) REVERT: H 175 MET cc_start: 0.8499 (mmt) cc_final: 0.8268 (mmt) outliers start: 25 outliers final: 15 residues processed: 292 average time/residue: 0.4586 time to fit residues: 193.1946 Evaluate side-chains 284 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 267 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 0.6980 chunk 207 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN F 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119713 restraints weight = 20070.949| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.15 r_work: 0.3091 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17785 Z= 0.145 Angle : 0.557 12.663 24005 Z= 0.275 Chirality : 0.045 0.244 2660 Planarity : 0.004 0.051 3125 Dihedral : 7.866 136.225 2617 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.37 % Allowed : 12.53 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2228 helix: 1.50 (0.18), residues: 933 sheet: 0.01 (0.29), residues: 312 loop : -0.65 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 24 HIS 0.005 0.001 HIS E 69 PHE 0.023 0.001 PHE G 347 TYR 0.014 0.001 TYR C 203 ARG 0.007 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 815) hydrogen bonds : angle 4.38297 ( 2352) metal coordination : bond 0.00490 ( 8) metal coordination : angle 3.49442 ( 12) covalent geometry : bond 0.00349 (17775) covalent geometry : angle 0.55177 (23993) Misc. bond : bond 0.00031 ( 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 290 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7474 (mmtt) REVERT: A 236 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 124 MET cc_start: 0.8146 (mtp) cc_final: 0.7566 (mpp) REVERT: B 149 ASP cc_start: 0.8122 (t0) cc_final: 0.7401 (t0) REVERT: C 58 LYS cc_start: 0.8514 (mttp) cc_final: 0.8254 (mmmt) REVERT: C 123 MET cc_start: 0.5725 (mmp) cc_final: 0.5287 (mmp) REVERT: C 200 MET cc_start: 0.7341 (ppp) cc_final: 0.6808 (ppp) REVERT: C 324 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7274 (mmmt) REVERT: D 40 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7574 (mt-10) REVERT: D 42 ASN cc_start: 0.8506 (t0) cc_final: 0.8177 (t0) REVERT: D 44 GLU cc_start: 0.8235 (mp0) cc_final: 0.7895 (mm-30) REVERT: D 118 MET cc_start: 0.8129 (ttp) cc_final: 0.7855 (mtm) REVERT: E 154 LYS cc_start: 0.8859 (mptt) cc_final: 0.8332 (mmpt) REVERT: E 219 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8447 (ttt) REVERT: E 251 MET cc_start: 0.8114 (mtt) cc_final: 0.7860 (mtt) REVERT: F 90 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7356 (p) REVERT: G 96 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7786 (mm-30) REVERT: G 203 TYR cc_start: 0.8087 (t80) cc_final: 0.7608 (t80) REVERT: G 204 LEU cc_start: 0.7831 (mt) cc_final: 0.7297 (mp) REVERT: G 206 ASN cc_start: 0.8173 (t0) cc_final: 0.7859 (m-40) REVERT: G 324 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7678 (mtpt) REVERT: G 331 ARG cc_start: 0.8298 (ttt180) cc_final: 0.8003 (ttt-90) REVERT: G 343 ASP cc_start: 0.7581 (t0) cc_final: 0.7275 (t0) REVERT: H 26 LYS cc_start: 0.7603 (mptt) cc_final: 0.6311 (ttpp) REVERT: H 41 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7390 (ptp-170) REVERT: H 76 GLU cc_start: 0.8266 (mp0) cc_final: 0.7626 (pm20) REVERT: H 175 MET cc_start: 0.8561 (mmt) cc_final: 0.8310 (mmt) outliers start: 25 outliers final: 22 residues processed: 274 average time/residue: 0.4195 time to fit residues: 165.1664 Evaluate side-chains 284 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 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 82 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 135 VAL 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 118 MET Chi-restraints excluded: chain H residue 192 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 109 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 185 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 133 optimal weight: 0.0050 chunk 24 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.168852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127918 restraints weight = 19701.012| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.02 r_work: 0.3143 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17785 Z= 0.117 Angle : 0.541 12.639 24005 Z= 0.267 Chirality : 0.044 0.232 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.810 137.301 2617 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.65 % Allowed : 12.31 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2228 helix: 1.57 (0.18), residues: 933 sheet: -0.06 (0.29), residues: 318 loop : -0.57 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 24 HIS 0.004 0.001 HIS E 69 PHE 0.031 0.001 PHE G 347 TYR 0.013 0.001 TYR C 203 ARG 0.010 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 815) hydrogen bonds : angle 4.31906 ( 2352) metal coordination : bond 0.00426 ( 8) metal coordination : angle 3.36750 ( 12) covalent geometry : bond 0.00273 (17775) covalent geometry : angle 0.53575 (23993) Misc. bond : bond 0.00020 ( 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: 30 poor density : 267 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8594 (tpp) cc_final: 0.8307 (tpp) REVERT: A 219 MET cc_start: 0.7776 (ttp) cc_final: 0.7464 (ttm) REVERT: A 236 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8135 (mt) REVERT: B 124 MET cc_start: 0.8117 (mtp) cc_final: 0.7467 (mpp) REVERT: B 149 ASP cc_start: 0.8163 (t0) cc_final: 0.7449 (t0) REVERT: C 58 LYS cc_start: 0.8507 (mttp) cc_final: 0.8250 (mmmt) REVERT: C 123 MET cc_start: 0.5707 (mmp) cc_final: 0.5173 (mmp) REVERT: C 200 MET cc_start: 0.7322 (ppp) cc_final: 0.6797 (ppp) REVERT: C 324 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7284 (mmmt) REVERT: D 34 LEU cc_start: 0.9215 (mt) cc_final: 0.8823 (mt) REVERT: D 40 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7501 (mt-10) REVERT: D 42 ASN cc_start: 0.8508 (t0) cc_final: 0.8171 (t0) REVERT: D 44 GLU cc_start: 0.8201 (mp0) cc_final: 0.7879 (mm-30) REVERT: D 118 MET cc_start: 0.8094 (ttp) cc_final: 0.7869 (mtm) REVERT: E 154 LYS cc_start: 0.8851 (mptt) cc_final: 0.8352 (mmpt) REVERT: E 219 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8345 (ttt) REVERT: F 90 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7313 (p) REVERT: G 96 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7774 (mm-30) REVERT: G 203 TYR cc_start: 0.8057 (t80) cc_final: 0.7578 (t80) REVERT: G 204 LEU cc_start: 0.7848 (mt) cc_final: 0.7394 (mp) REVERT: G 206 ASN cc_start: 0.8160 (t0) cc_final: 0.7846 (m-40) REVERT: G 234 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7541 (ttp-170) REVERT: G 278 LEU cc_start: 0.8101 (mp) cc_final: 0.7891 (mm) REVERT: G 324 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7777 (mtpt) REVERT: G 331 ARG cc_start: 0.8240 (ttt180) cc_final: 0.7952 (ttt-90) REVERT: G 343 ASP cc_start: 0.7571 (t0) cc_final: 0.7279 (t0) REVERT: H 26 LYS cc_start: 0.7558 (mptt) cc_final: 0.6328 (ttpp) REVERT: H 41 ARG cc_start: 0.7855 (ptp-110) cc_final: 0.7370 (ptp-170) REVERT: H 76 GLU cc_start: 0.8236 (mp0) cc_final: 0.7614 (pm20) REVERT: H 175 MET cc_start: 0.8519 (mmt) cc_final: 0.8291 (mmt) outliers start: 30 outliers final: 25 residues processed: 279 average time/residue: 0.3388 time to fit residues: 136.8510 Evaluate side-chains 290 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 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 82 ILE 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 192 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 90 THR 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 38 ASP Chi-restraints excluded: chain G residue 265 VAL 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 118 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 207 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 163 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 218 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122307 restraints weight = 20125.741| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.12 r_work: 0.3097 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 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 = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2536 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= 0.133 Angle : 0.560 14.926 24005 Z= 0.274 Chirality : 0.045 0.232 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.781 136.436 2617 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.70 % Allowed : 12.64 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2228 helix: 1.54 (0.18), residues: 933 sheet: 0.04 (0.29), residues: 322 loop : -0.61 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 24 HIS 0.004 0.001 HIS E 69 PHE 0.027 0.001 PHE G 347 TYR 0.016 0.001 TYR E 222 ARG 0.007 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 815) hydrogen bonds : angle 4.33009 ( 2352) metal coordination : bond 0.00467 ( 8) metal coordination : angle 3.22643 ( 12) covalent geometry : bond 0.00320 (17775) covalent geometry : angle 0.55578 (23993) 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 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7849 (ptmt) cc_final: 0.7469 (mmtt) REVERT: A 219 MET cc_start: 0.7877 (ttp) cc_final: 0.7584 (ttm) REVERT: A 236 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8155 (mt) REVERT: B 149 ASP cc_start: 0.8133 (t0) cc_final: 0.7418 (t0) REVERT: C 58 LYS cc_start: 0.8546 (mttp) cc_final: 0.8286 (mmmt) REVERT: C 123 MET cc_start: 0.5793 (mmp) cc_final: 0.5239 (mmp) REVERT: C 200 MET cc_start: 0.7297 (ppp) cc_final: 0.6803 (ppp) REVERT: C 324 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7322 (mmmt) REVERT: D 34 LEU cc_start: 0.9258 (mt) cc_final: 0.8868 (mt) REVERT: D 40 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7434 (mt-10) REVERT: D 42 ASN cc_start: 0.8522 (t0) cc_final: 0.8219 (t0) REVERT: D 44 GLU cc_start: 0.8257 (mp0) cc_final: 0.7905 (mm-30) REVERT: D 118 MET cc_start: 0.8110 (ttp) cc_final: 0.7888 (mtm) REVERT: E 154 LYS cc_start: 0.8875 (mptt) cc_final: 0.8367 (mmpt) REVERT: E 219 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8579 (ttt) REVERT: F 90 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7383 (p) REVERT: G 96 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7768 (mm-30) REVERT: G 203 TYR cc_start: 0.8094 (t80) cc_final: 0.7619 (t80) REVERT: G 204 LEU cc_start: 0.7906 (mt) cc_final: 0.7471 (mp) REVERT: G 206 ASN cc_start: 0.8190 (t0) cc_final: 0.7894 (m-40) REVERT: G 278 LEU cc_start: 0.8168 (mp) cc_final: 0.7937 (mm) REVERT: G 324 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7758 (mtpt) REVERT: G 331 ARG cc_start: 0.8276 (ttt180) cc_final: 0.8055 (ttt-90) REVERT: G 343 ASP cc_start: 0.7633 (t0) cc_final: 0.7317 (t0) REVERT: H 26 LYS cc_start: 0.7606 (mptt) cc_final: 0.6387 (ttpp) REVERT: H 41 ARG cc_start: 0.7920 (ptp-110) cc_final: 0.7439 (ptp-170) REVERT: H 76 GLU cc_start: 0.8261 (mp0) cc_final: 0.7634 (pm20) REVERT: H 175 MET cc_start: 0.8581 (mmt) cc_final: 0.8335 (mmt) outliers start: 31 outliers final: 26 residues processed: 278 average time/residue: 0.3424 time to fit residues: 137.8803 Evaluate side-chains 292 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 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 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 192 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 90 THR 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 38 ASP Chi-restraints excluded: chain G residue 265 VAL 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 118 MET Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 210 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 39 optimal weight: 0.1980 chunk 215 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 185 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.165303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123686 restraints weight = 20053.100| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.06 r_work: 0.3091 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17785 Z= 0.116 Angle : 0.543 13.642 24005 Z= 0.267 Chirality : 0.044 0.233 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.728 136.533 2617 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.59 % Allowed : 12.69 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2228 helix: 1.60 (0.18), residues: 933 sheet: 0.01 (0.29), residues: 342 loop : -0.54 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 61 HIS 0.006 0.001 HIS G 236 PHE 0.032 0.001 PHE G 347 TYR 0.017 0.001 TYR E 222 ARG 0.008 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 815) hydrogen bonds : angle 4.30950 ( 2352) metal coordination : bond 0.00416 ( 8) metal coordination : angle 3.21200 ( 12) covalent geometry : bond 0.00273 (17775) covalent geometry : angle 0.53836 (23993) Misc. bond : bond 0.00020 ( 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 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7790 (ttp) cc_final: 0.7476 (ttm) REVERT: A 236 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8113 (mt) REVERT: B 124 MET cc_start: 0.8110 (mtp) cc_final: 0.7537 (mpt) REVERT: B 149 ASP cc_start: 0.8179 (t0) cc_final: 0.7463 (t0) REVERT: C 58 LYS cc_start: 0.8545 (mttp) cc_final: 0.8248 (mmmt) REVERT: C 123 MET cc_start: 0.5793 (mmp) cc_final: 0.5229 (mmp) REVERT: C 200 MET cc_start: 0.7286 (ppp) cc_final: 0.6798 (ppp) REVERT: C 324 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7256 (mmmt) REVERT: D 34 LEU cc_start: 0.9271 (mt) cc_final: 0.8890 (mt) REVERT: D 40 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7465 (mt-10) REVERT: D 42 ASN cc_start: 0.8514 (t0) cc_final: 0.8208 (t0) REVERT: D 44 GLU cc_start: 0.8219 (mp0) cc_final: 0.7878 (mm-30) REVERT: D 118 MET cc_start: 0.8100 (ttp) cc_final: 0.7864 (mtm) REVERT: E 154 LYS cc_start: 0.8842 (mptt) cc_final: 0.8304 (mmpt) REVERT: E 219 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8393 (ttt) REVERT: E 282 MET cc_start: 0.7674 (tpp) cc_final: 0.7166 (tpt) REVERT: F 90 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7306 (p) REVERT: G 96 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7803 (mm-30) REVERT: G 203 TYR cc_start: 0.8097 (t80) cc_final: 0.7616 (t80) REVERT: G 204 LEU cc_start: 0.7856 (mt) cc_final: 0.7467 (mp) REVERT: G 206 ASN cc_start: 0.8175 (t0) cc_final: 0.7842 (m-40) REVERT: G 324 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7718 (mtpt) REVERT: G 331 ARG cc_start: 0.8245 (ttt180) cc_final: 0.8000 (ttt-90) REVERT: G 343 ASP cc_start: 0.7619 (t0) cc_final: 0.7285 (t0) REVERT: H 26 LYS cc_start: 0.7551 (mptt) cc_final: 0.6303 (ttpp) REVERT: H 41 ARG cc_start: 0.7885 (ptp-110) cc_final: 0.7403 (ptp-170) REVERT: H 76 GLU cc_start: 0.8245 (mp0) cc_final: 0.7610 (pm20) REVERT: H 175 MET cc_start: 0.8534 (mmt) cc_final: 0.8313 (mmt) REVERT: H 203 MET cc_start: 0.8604 (mtp) cc_final: 0.8299 (mtp) outliers start: 29 outliers final: 24 residues processed: 280 average time/residue: 0.3650 time to fit residues: 148.9520 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 : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 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 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 192 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 90 THR 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 38 ASP Chi-restraints excluded: chain G residue 265 VAL 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 118 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 31 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 214 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN C 237 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 = 0.163056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120768 restraints weight = 20047.285| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.14 r_work: 0.3127 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2640 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 : 0.555 14.746 24005 Z= 0.272 Chirality : 0.045 0.233 2660 Planarity : 0.004 0.050 3125 Dihedral : 7.697 135.445 2617 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.54 % Allowed : 12.86 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2228 helix: 1.59 (0.18), residues: 933 sheet: -0.02 (0.29), residues: 342 loop : -0.55 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 238 HIS 0.005 0.001 HIS E 69 PHE 0.028 0.001 PHE G 347 TYR 0.016 0.001 TYR E 222 ARG 0.007 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 815) hydrogen bonds : angle 4.31346 ( 2352) metal coordination : bond 0.00440 ( 8) metal coordination : angle 3.12244 ( 12) covalent geometry : bond 0.00305 (17775) covalent geometry : angle 0.55043 (23993) Misc. bond : bond 0.00025 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12648.72 seconds wall clock time: 222 minutes 40.17 seconds (13360.17 seconds total)