Starting phenix.real_space_refine on Sun Aug 24 05:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxz_42790/08_2025/8uxz_42790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxz_42790/08_2025/8uxz_42790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxz_42790/08_2025/8uxz_42790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxz_42790/08_2025/8uxz_42790.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxz_42790/08_2025/8uxz_42790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxz_42790/08_2025/8uxz_42790_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17474 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2452 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 584 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "C" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3433 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 424} Chain: "D" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2173 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 267} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2452 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain: "F" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 584 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "G" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3433 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 424} Chain: "H" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2006 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6679 SG CYS D 27 57.470 109.362 72.805 1.00 56.12 S ATOM 6699 SG CYS D 30 56.295 106.297 70.977 1.00 78.81 S ATOM 6830 SG CYS D 46 59.667 107.835 70.025 1.00 64.26 S ATOM 6852 SG CYS D 49 56.547 109.679 69.155 1.00 61.41 S ATOM 15154 SG CYS H 27 21.731 163.794 44.849 1.00 73.80 S ATOM 15174 SG CYS H 30 18.512 163.861 46.761 1.00 75.44 S ATOM 15305 SG CYS H 46 21.309 166.361 47.595 1.00 67.77 S ATOM 15327 SG CYS H 49 21.846 162.767 48.490 1.00 69.44 S Time building chain proxies: 4.29, per 1000 atoms: 0.25 Number of scatterers: 17474 At special positions: 0 Unit cell: (106.015, 191.288, 118.691, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 126 16.00 P 10 15.00 Mg 2 11.99 O 3276 8.00 N 3082 7.00 C 10976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 676.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 27 " 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 46 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 27 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 49 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 30 " 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: 90 helices and 25 sheets defined 44.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 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 29 Processing helix chain 'A' and resid 32 through 55 removed outlier: 3.531A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 136 through 153 removed outlier: 3.636A pdb=" N TYR A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.797A 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 237 Processing helix chain 'A' and resid 243 through 252 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 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' 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 191 removed outlier: 3.780A pdb=" N LEU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY D 191 " --> pdb=" O MET D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.663A pdb=" N SER D 207 " --> pdb=" O MET D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 4.335A 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 254 removed outlier: 3.819A pdb=" N GLU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 279 removed outlier: 4.226A pdb=" N ARG D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU D 268 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 9 through 29 Processing helix chain 'E' and resid 32 through 55 removed outlier: 3.659A pdb=" N ILE E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 136 through 153 removed outlier: 3.591A pdb=" N TYR E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.822A 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 237 Processing helix chain 'E' and resid 243 through 252 Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 278 through 298 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: 3.853A 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: 3.543A 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 166 through 169 Processing helix chain 'H' and resid 170 through 191 removed outlier: 3.534A pdb=" N LEU H 174 " --> pdb=" O ALA H 170 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) removed outlier: 4.188A 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: 3.980A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 265 through 279 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 4.598A pdb=" N PHE A 86 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 105 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 88 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY A 103 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ILE A 158 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET A 114 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 160 " --> pdb=" O MET A 114 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 116 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 157 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR A 198 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR A 159 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 195 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN A 218 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS A 197 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 220 " --> pdb=" O CYS A 197 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 217 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE A 268 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.660A 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 removed outlier: 6.593A pdb=" N GLY A 203 " --> pdb=" O SER A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 85 removed outlier: 3.562A pdb=" N VAL B 153 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 85 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 137 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 135 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN B 107 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.795A pdb=" N ILE B 127 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 117 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN B 125 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B 119 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.840A 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: 8.025A 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: 4.547A 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: 4.472A pdb=" N ASP C 229 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 6.967A 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: 4.547A 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: 4.472A pdb=" N ASP C 229 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 6.967A 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: 7.734A 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: 4.559A pdb=" N VAL D 110 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 122 " --> pdb=" O MET D 111 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ILE D 157 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 121 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE D 159 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA D 123 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA D 161 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE D 125 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU D 156 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL D 197 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS D 158 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR D 199 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER D 160 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 216 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 259 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 89 removed outlier: 5.700A pdb=" N GLU E 85 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG E 107 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY E 103 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE E 158 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET E 114 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE E 160 " --> pdb=" O MET E 114 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE E 116 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE E 157 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR E 198 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 6.260A 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: 8.090A pdb=" N ASN E 218 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS E 197 " --> pdb=" O ASN E 218 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU E 220 " --> pdb=" O CYS E 197 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL E 217 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE E 268 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 6.644A 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: 6.645A pdb=" N HIS F 81 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL F 154 " --> pdb=" O HIS F 81 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 83 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL F 135 " --> pdb=" O GLN F 107 " (cutoff:3.500A) removed outlier: 5.590A 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: 3.849A pdb=" N CYS F 116 " --> pdb=" O ILE F 127 " (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: 8.111A 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: 7.066A 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: 6.408A 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: 6.411A 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: 3.736A 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: 6.877A 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: 10.650A pdb=" N ASN G 340 " --> pdb=" O GLN G 237 " (cutoff:3.500A) removed outlier: 6.839A 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: 4.363A pdb=" N VAL H 110 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA H 122 " --> pdb=" O MET H 111 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU H 156 " --> pdb=" O ILE H 195 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL H 197 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N CYS H 158 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR H 199 " --> pdb=" O CYS H 158 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER H 160 " --> pdb=" O THR H 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 218 through 219 817 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3357 1.33 - 1.45: 4094 1.45 - 1.58: 10096 1.58 - 1.71: 10 1.71 - 1.83: 218 Bond restraints: 17775 Sorted by residual: bond pdb=" C VAL D 23 " pdb=" N TRP D 24 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.44e-02 4.82e+03 9.22e+00 bond pdb=" N ASP F 130 " pdb=" CA ASP F 130 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.43e+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 6.32e+00 bond pdb=" N SER F 132 " pdb=" CA SER F 132 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.27e+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 6.24e+00 ... (remaining 17770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 23636 1.88 - 3.76: 299 3.76 - 5.64: 42 5.64 - 7.52: 10 7.52 - 9.41: 6 Bond angle restraints: 23993 Sorted by residual: angle pdb=" CA SER F 132 " pdb=" C SER F 132 " pdb=" O SER F 132 " ideal model delta sigma weight residual 121.56 117.91 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" CA THR D 199 " pdb=" C THR D 199 " pdb=" O THR D 199 " ideal model delta sigma weight residual 121.56 117.54 4.02 1.21e+00 6.83e-01 1.11e+01 angle pdb=" CA GLU H 44 " pdb=" C GLU H 44 " pdb=" O GLU H 44 " ideal model delta sigma weight residual 121.54 117.78 3.76 1.16e+00 7.43e-01 1.05e+01 angle pdb=" N GLU D 265 " pdb=" CA GLU D 265 " pdb=" C GLU D 265 " ideal model delta sigma weight residual 113.38 109.45 3.93 1.23e+00 6.61e-01 1.02e+01 angle pdb=" C2' ADP G 501 " pdb=" C3' ADP G 501 " pdb=" C4' ADP G 501 " ideal model delta sigma weight residual 111.00 101.59 9.41 3.00e+00 1.11e-01 9.83e+00 ... (remaining 23988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 10706 28.72 - 57.44: 256 57.44 - 86.15: 34 86.15 - 114.87: 1 114.87 - 143.59: 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 300.00 156.41 143.59 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 300.00 156.56 143.44 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 57.86 -117.86 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 10998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2392 0.075 - 0.150: 257 0.150 - 0.225: 7 0.225 - 0.300: 2 0.300 - 0.375: 2 Chirality restraints: 2660 Sorted by residual: chirality pdb=" CA HIS A 276 " pdb=" N HIS A 276 " pdb=" C HIS A 276 " pdb=" CB HIS A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA HIS E 276 " pdb=" N HIS E 276 " pdb=" C HIS E 276 " pdb=" CB HIS E 276 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 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 1.68e+00 ... (remaining 2657 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN F 201 " 0.020 2.00e-02 2.50e+03 8.42e-02 1.06e+02 pdb=" C4 BTN F 201 " -0.135 2.00e-02 2.50e+03 pdb=" C5 BTN F 201 " 0.050 2.00e-02 2.50e+03 pdb=" N1 BTN F 201 " -0.001 2.00e-02 2.50e+03 pdb=" N2 BTN F 201 " 0.131 2.00e-02 2.50e+03 pdb=" O3 BTN F 201 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN B 201 " 0.026 2.00e-02 2.50e+03 8.34e-02 1.04e+02 pdb=" C4 BTN B 201 " -0.064 2.00e-02 2.50e+03 pdb=" C5 BTN B 201 " -0.069 2.00e-02 2.50e+03 pdb=" N1 BTN B 201 " 0.106 2.00e-02 2.50e+03 pdb=" N2 BTN B 201 " 0.103 2.00e-02 2.50e+03 pdb=" O3 BTN B 201 " -0.102 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 1.13e-02 3.51e+00 pdb=" C2 ADP G 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ADP G 501 " 0.001 2.00e-02 2.50e+03 pdb=" C5 ADP G 501 " -0.005 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 " -0.012 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 161 2.58 - 3.16: 14528 3.16 - 3.74: 26499 3.74 - 4.32: 37939 4.32 - 4.90: 65244 Nonbonded interactions: 144371 Sorted by model distance: nonbonded pdb=" O2A ADP C 501 " pdb="MG MG C 502 " model vdw 1.999 2.170 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 2.203 3.040 nonbonded pdb=" O GLY A 133 " pdb=" OG1 THR A 163 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR C 154 " pdb=" OD1 ASP C 175 " model vdw 2.235 3.040 ... (remaining 144366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 23 through 302) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.580 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 0.101 17785 Z= 0.195 Angle : 0.568 9.406 24005 Z= 0.300 Chirality : 0.046 0.375 2660 Planarity : 0.004 0.084 3125 Dihedral : 12.835 143.589 6893 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.19), residues: 2228 helix: 1.77 (0.18), residues: 903 sheet: 0.08 (0.29), residues: 331 loop : -0.60 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 309 TYR 0.017 0.001 TYR E 225 PHE 0.011 0.001 PHE D 125 TRP 0.005 0.001 TRP I 3 HIS 0.004 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00361 (17775) covalent geometry : angle 0.56606 (23993) hydrogen bonds : bond 0.16527 ( 804) hydrogen bonds : angle 6.53370 ( 2319) metal coordination : bond 0.00380 ( 8) metal coordination : angle 2.26609 ( 12) Misc. bond : bond 0.07798 ( 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 408 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8900 (t80) cc_final: 0.8596 (t80) REVERT: A 151 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7776 (tt0) REVERT: A 154 LYS cc_start: 0.8533 (mptt) cc_final: 0.8263 (mmtp) REVERT: A 173 GLU cc_start: 0.8195 (tp30) cc_final: 0.7894 (mm-30) REVERT: A 216 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8513 (mmtm) REVERT: C 87 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 197 MET cc_start: 0.6044 (ttm) cc_final: 0.5711 (tpt) REVERT: C 203 TYR cc_start: 0.7180 (t80) cc_final: 0.6909 (t80) REVERT: C 232 MET cc_start: 0.8548 (mmt) cc_final: 0.8169 (tpp) REVERT: C 239 VAL cc_start: 0.9012 (t) cc_final: 0.8709 (m) REVERT: C 280 GLU cc_start: 0.7722 (tt0) cc_final: 0.7288 (tt0) REVERT: D 274 LEU cc_start: 0.9167 (mt) cc_final: 0.8954 (mt) REVERT: E 50 LEU cc_start: 0.7773 (tp) cc_final: 0.7572 (tp) REVERT: E 97 ASP cc_start: 0.7951 (p0) cc_final: 0.7668 (p0) REVERT: E 154 LYS cc_start: 0.8792 (mptt) cc_final: 0.8560 (mmtt) REVERT: E 219 MET cc_start: 0.7730 (ttm) cc_final: 0.7517 (ttm) REVERT: E 301 SER cc_start: 0.6707 (t) cc_final: 0.6062 (p) REVERT: F 123 MET cc_start: 0.6909 (mtp) cc_final: 0.6554 (mtt) REVERT: G 23 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6924 (mt-10) REVERT: G 27 LYS cc_start: 0.8529 (mttt) cc_final: 0.8233 (mtmt) REVERT: G 38 ASP cc_start: 0.7540 (m-30) cc_final: 0.7204 (t0) REVERT: G 128 VAL cc_start: 0.8668 (t) cc_final: 0.8234 (p) REVERT: G 159 LYS cc_start: 0.6229 (mtpt) cc_final: 0.5913 (mtmm) REVERT: G 258 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6739 (mm-30) REVERT: G 286 PHE cc_start: 0.8262 (t80) cc_final: 0.7150 (t80) REVERT: G 302 MET cc_start: 0.8833 (mtp) cc_final: 0.8304 (mtp) REVERT: G 324 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7391 (mptt) REVERT: G 408 GLU cc_start: 0.8698 (tt0) cc_final: 0.8459 (tt0) REVERT: G 425 MET cc_start: 0.8548 (mmp) cc_final: 0.8043 (mmt) REVERT: G 428 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7090 (mm-30) REVERT: H 25 THR cc_start: 0.7529 (p) cc_final: 0.6955 (m) REVERT: H 175 MET cc_start: 0.8865 (mmt) cc_final: 0.8573 (mmt) REVERT: H 186 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7896 (mptt) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1720 time to fit residues: 99.1823 Evaluate side-chains 266 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN C 94 GLN C 219 GLN C 221 ASN G 94 GLN H 153 ASN H 176 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130862 restraints weight = 19289.634| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.98 r_work: 0.3176 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17785 Z= 0.165 Angle : 0.582 8.243 24005 Z= 0.298 Chirality : 0.046 0.253 2660 Planarity : 0.005 0.052 3125 Dihedral : 8.941 125.178 2617 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.65 % Allowed : 6.48 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2228 helix: 1.59 (0.18), residues: 928 sheet: 0.49 (0.30), residues: 314 loop : -0.58 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 36 TYR 0.019 0.001 TYR E 225 PHE 0.017 0.002 PHE E 8 TRP 0.005 0.001 TRP D 24 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00385 (17775) covalent geometry : angle 0.58062 (23993) hydrogen bonds : bond 0.04387 ( 804) hydrogen bonds : angle 4.99196 ( 2319) metal coordination : bond 0.00573 ( 8) metal coordination : angle 1.99748 ( 12) Misc. bond : bond 0.00241 ( 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 319 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8876 (t80) cc_final: 0.8539 (t80) REVERT: A 151 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7862 (tt0) REVERT: A 154 LYS cc_start: 0.8586 (mptt) cc_final: 0.8229 (mmtt) REVERT: A 216 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8206 (mmtm) REVERT: A 261 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7083 (tt) REVERT: A 293 ASP cc_start: 0.7379 (m-30) cc_final: 0.7121 (t0) REVERT: C 87 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 197 MET cc_start: 0.5972 (ttm) cc_final: 0.5708 (tpt) REVERT: C 203 TYR cc_start: 0.6443 (t80) cc_final: 0.5876 (t80) REVERT: C 280 GLU cc_start: 0.7722 (tt0) cc_final: 0.7405 (tt0) REVERT: C 443 LYS cc_start: 0.7328 (tttp) cc_final: 0.7125 (tttp) REVERT: D 234 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 274 LEU cc_start: 0.9002 (mt) cc_final: 0.8777 (mt) REVERT: D 278 MET cc_start: 0.8306 (mmm) cc_final: 0.8069 (mmm) REVERT: E 50 LEU cc_start: 0.7641 (tp) cc_final: 0.7398 (tp) REVERT: E 154 LYS cc_start: 0.8875 (mptt) cc_final: 0.8492 (mmtt) REVERT: E 219 MET cc_start: 0.8106 (ttm) cc_final: 0.7876 (mtp) REVERT: F 123 MET cc_start: 0.6848 (mtp) cc_final: 0.6539 (mtt) REVERT: G 23 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6847 (mt-10) REVERT: G 27 LYS cc_start: 0.8579 (mttt) cc_final: 0.8324 (mtmt) REVERT: G 159 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6885 (mtmm) REVERT: G 184 MET cc_start: 0.7527 (tmm) cc_final: 0.7253 (tmm) REVERT: G 239 VAL cc_start: 0.8933 (t) cc_final: 0.8685 (m) REVERT: G 258 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7121 (mm-30) REVERT: G 286 PHE cc_start: 0.8544 (t80) cc_final: 0.7475 (t80) REVERT: G 324 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7655 (mptt) REVERT: G 327 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7610 (tt0) REVERT: H 84 LYS cc_start: 0.6291 (mmtt) cc_final: 0.5937 (mtpt) REVERT: H 186 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7415 (mptt) outliers start: 30 outliers final: 18 residues processed: 303 average time/residue: 0.1775 time to fit residues: 76.2663 Evaluate side-chains 279 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 169 MET Chi-restraints excluded: chain G residue 262 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 70 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 211 optimal weight: 0.0670 chunk 161 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 218 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 221 GLN B 81 HIS C 329 HIS E 177 GLN E 221 GLN ** G 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.173494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129936 restraints weight = 19465.549| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.05 r_work: 0.3183 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 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 = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2078 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= 0.140 Angle : 0.550 8.779 24005 Z= 0.276 Chirality : 0.045 0.242 2660 Planarity : 0.004 0.044 3125 Dihedral : 8.586 117.259 2617 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.37 % Allowed : 8.02 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2228 helix: 1.70 (0.17), residues: 921 sheet: 0.77 (0.32), residues: 294 loop : -0.69 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 36 TYR 0.020 0.001 TYR H 35 PHE 0.015 0.001 PHE E 8 TRP 0.004 0.001 TRP E 238 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00329 (17775) covalent geometry : angle 0.54381 (23993) hydrogen bonds : bond 0.03600 ( 804) hydrogen bonds : angle 4.58465 ( 2319) metal coordination : bond 0.00651 ( 8) metal coordination : angle 3.84291 ( 12) Misc. bond : bond 0.00068 ( 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 304 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5300 (t) cc_final: 0.5035 (p) REVERT: A 95 TYR cc_start: 0.8849 (t80) cc_final: 0.8364 (t80) REVERT: A 151 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7861 (tt0) REVERT: A 154 LYS cc_start: 0.8511 (mptt) cc_final: 0.8128 (mmtt) REVERT: A 216 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8199 (mmtm) REVERT: A 293 ASP cc_start: 0.7279 (m-30) cc_final: 0.6921 (t0) REVERT: C 87 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8244 (mt-10) REVERT: C 197 MET cc_start: 0.5900 (ttm) cc_final: 0.5541 (tpt) REVERT: C 203 TYR cc_start: 0.6620 (t80) cc_final: 0.5992 (t80) REVERT: C 211 GLU cc_start: 0.8470 (pt0) cc_final: 0.8235 (pt0) REVERT: C 280 GLU cc_start: 0.7639 (tt0) cc_final: 0.7268 (tt0) REVERT: D 274 LEU cc_start: 0.8876 (mt) cc_final: 0.8643 (mt) REVERT: D 278 MET cc_start: 0.8343 (mmm) cc_final: 0.8093 (mmm) REVERT: E 50 LEU cc_start: 0.7672 (tp) cc_final: 0.7439 (tp) REVERT: E 154 LYS cc_start: 0.8888 (mptt) cc_final: 0.8503 (mmtt) REVERT: E 219 MET cc_start: 0.8207 (ttm) cc_final: 0.7996 (mtp) REVERT: F 123 MET cc_start: 0.6865 (mtp) cc_final: 0.6565 (mtt) REVERT: G 23 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6981 (mt-10) REVERT: G 27 LYS cc_start: 0.8596 (mttt) cc_final: 0.8359 (mtmt) REVERT: G 123 MET cc_start: 0.6537 (mmp) cc_final: 0.6269 (mmp) REVERT: G 159 LYS cc_start: 0.7393 (mtpt) cc_final: 0.6719 (mtmm) REVERT: G 184 MET cc_start: 0.7617 (tmm) cc_final: 0.7297 (tmm) REVERT: G 239 VAL cc_start: 0.8924 (t) cc_final: 0.8674 (m) REVERT: G 258 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7118 (mm-30) REVERT: G 286 PHE cc_start: 0.8561 (t80) cc_final: 0.7534 (t80) REVERT: G 324 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7647 (mptt) REVERT: G 408 GLU cc_start: 0.8678 (tt0) cc_final: 0.8380 (mt-10) REVERT: H 111 MET cc_start: 0.8819 (mtp) cc_final: 0.8575 (mtp) REVERT: H 153 ASN cc_start: 0.7302 (p0) cc_final: 0.6738 (p0) outliers start: 25 outliers final: 19 residues processed: 292 average time/residue: 0.1502 time to fit residues: 64.0064 Evaluate side-chains 279 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 44 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 52 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS C 329 HIS F 126 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128433 restraints weight = 19385.238| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.01 r_work: 0.3175 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17785 Z= 0.140 Angle : 0.544 8.288 24005 Z= 0.272 Chirality : 0.045 0.232 2660 Planarity : 0.004 0.045 3125 Dihedral : 8.332 125.432 2617 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.92 % Allowed : 9.23 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2228 helix: 1.68 (0.17), residues: 930 sheet: 0.59 (0.31), residues: 304 loop : -0.72 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 36 TYR 0.022 0.001 TYR A 225 PHE 0.012 0.001 PHE E 8 TRP 0.006 0.001 TRP D 24 HIS 0.005 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00331 (17775) covalent geometry : angle 0.53842 (23993) hydrogen bonds : bond 0.03365 ( 804) hydrogen bonds : angle 4.41868 ( 2319) metal coordination : bond 0.00580 ( 8) metal coordination : angle 3.53270 ( 12) Misc. bond : bond 0.00020 ( 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 316 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5267 (t) cc_final: 0.5043 (p) REVERT: A 95 TYR cc_start: 0.8848 (t80) cc_final: 0.8379 (t80) REVERT: A 151 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7842 (tt0) REVERT: A 154 LYS cc_start: 0.8449 (mptt) cc_final: 0.8054 (mmtt) REVERT: A 216 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8149 (mmtm) REVERT: C 87 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8268 (mt-10) REVERT: C 184 MET cc_start: 0.6838 (ppp) cc_final: 0.6633 (mtp) REVERT: C 197 MET cc_start: 0.5889 (ttm) cc_final: 0.5532 (tpt) REVERT: C 203 TYR cc_start: 0.6536 (t80) cc_final: 0.5913 (t80) REVERT: C 280 GLU cc_start: 0.7669 (tt0) cc_final: 0.7314 (tt0) REVERT: C 384 MET cc_start: 0.8672 (ttt) cc_final: 0.8438 (ttt) REVERT: C 429 ASN cc_start: 0.7579 (m-40) cc_final: 0.7178 (m-40) REVERT: D 274 LEU cc_start: 0.8838 (mt) cc_final: 0.8604 (mt) REVERT: D 278 MET cc_start: 0.8281 (mmm) cc_final: 0.8024 (mmm) REVERT: E 50 LEU cc_start: 0.7719 (tp) cc_final: 0.7498 (tp) REVERT: E 65 GLN cc_start: 0.8049 (mt0) cc_final: 0.7730 (mt0) REVERT: E 128 ILE cc_start: 0.8687 (mp) cc_final: 0.8456 (mp) REVERT: E 154 LYS cc_start: 0.8870 (mptt) cc_final: 0.8473 (mmtt) REVERT: E 219 MET cc_start: 0.8258 (ttm) cc_final: 0.8039 (mtp) REVERT: F 123 MET cc_start: 0.6789 (mtp) cc_final: 0.6482 (mtt) REVERT: G 15 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8432 (tt) REVERT: G 27 LYS cc_start: 0.8538 (mttt) cc_final: 0.8238 (mtmt) REVERT: G 184 MET cc_start: 0.7756 (tmm) cc_final: 0.7391 (tmm) REVERT: G 239 VAL cc_start: 0.8925 (t) cc_final: 0.8691 (m) REVERT: G 258 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7065 (mm-30) REVERT: G 324 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7509 (mptt) REVERT: G 408 GLU cc_start: 0.8694 (tt0) cc_final: 0.8449 (mt-10) REVERT: H 111 MET cc_start: 0.8786 (mtp) cc_final: 0.8544 (mtp) REVERT: H 153 ASN cc_start: 0.7597 (p0) cc_final: 0.6958 (p0) outliers start: 35 outliers final: 26 residues processed: 297 average time/residue: 0.1493 time to fit residues: 64.0184 Evaluate side-chains 288 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 64 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 31 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS C 329 HIS F 126 GLN G 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.172623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129181 restraints weight = 19359.771| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.93 r_work: 0.3150 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2512 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= 0.135 Angle : 0.532 8.707 24005 Z= 0.266 Chirality : 0.044 0.236 2660 Planarity : 0.004 0.045 3125 Dihedral : 8.058 128.735 2617 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.47 % Allowed : 9.01 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2228 helix: 1.71 (0.17), residues: 928 sheet: 0.65 (0.31), residues: 302 loop : -0.76 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 36 TYR 0.022 0.001 TYR A 225 PHE 0.023 0.001 PHE G 286 TRP 0.006 0.001 TRP E 238 HIS 0.005 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00319 (17775) covalent geometry : angle 0.52777 (23993) hydrogen bonds : bond 0.03208 ( 804) hydrogen bonds : angle 4.27395 ( 2319) metal coordination : bond 0.00425 ( 8) metal coordination : angle 3.12805 ( 12) Misc. bond : bond 0.00020 ( 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 323 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5252 (t) cc_final: 0.5028 (p) REVERT: A 95 TYR cc_start: 0.8865 (t80) cc_final: 0.8368 (t80) REVERT: A 151 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7804 (tt0) REVERT: A 154 LYS cc_start: 0.8512 (mptt) cc_final: 0.8122 (mmtt) REVERT: A 216 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8447 (mmtm) REVERT: A 293 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6836 (t0) REVERT: C 87 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 197 MET cc_start: 0.5972 (ttm) cc_final: 0.5705 (tpt) REVERT: C 280 GLU cc_start: 0.7815 (tt0) cc_final: 0.7495 (tt0) REVERT: C 331 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7416 (ttp80) REVERT: C 429 ASN cc_start: 0.7613 (m-40) cc_final: 0.7112 (m-40) REVERT: C 436 ASN cc_start: 0.7014 (OUTLIER) cc_final: 0.6734 (m-40) REVERT: D 118 MET cc_start: 0.8469 (ptp) cc_final: 0.8205 (ptt) REVERT: D 274 LEU cc_start: 0.8946 (mt) cc_final: 0.8702 (mt) REVERT: D 278 MET cc_start: 0.8371 (mmm) cc_final: 0.8118 (mmm) REVERT: E 50 LEU cc_start: 0.7847 (tp) cc_final: 0.7626 (tp) REVERT: E 65 GLN cc_start: 0.8101 (mt0) cc_final: 0.7811 (mt0) REVERT: E 154 LYS cc_start: 0.8877 (mptt) cc_final: 0.8507 (mmtt) REVERT: E 188 MET cc_start: 0.8972 (ttm) cc_final: 0.8690 (ttt) REVERT: E 219 MET cc_start: 0.8294 (ttm) cc_final: 0.8049 (mtp) REVERT: E 291 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (mm) REVERT: E 307 ASN cc_start: 0.8503 (m-40) cc_final: 0.8284 (m110) REVERT: F 123 MET cc_start: 0.6830 (mtp) cc_final: 0.6464 (mtt) REVERT: G 15 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8507 (tt) REVERT: G 27 LYS cc_start: 0.8682 (mttt) cc_final: 0.8427 (mtmt) REVERT: G 97 ARG cc_start: 0.7079 (mtt90) cc_final: 0.6560 (mtm110) REVERT: G 184 MET cc_start: 0.7604 (tmm) cc_final: 0.7304 (tmm) REVERT: G 239 VAL cc_start: 0.8915 (t) cc_final: 0.8683 (m) REVERT: G 258 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7126 (mm-30) REVERT: G 288 GLU cc_start: 0.7542 (pt0) cc_final: 0.7293 (pt0) REVERT: G 324 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7653 (mptt) REVERT: G 408 GLU cc_start: 0.8706 (tt0) cc_final: 0.8438 (mt-10) REVERT: H 62 HIS cc_start: 0.8161 (m90) cc_final: 0.7950 (m-70) REVERT: H 84 LYS cc_start: 0.6296 (mmtt) cc_final: 0.5911 (mtpt) REVERT: H 111 MET cc_start: 0.8817 (mtp) cc_final: 0.8585 (mtp) REVERT: H 153 ASN cc_start: 0.7667 (p0) cc_final: 0.6999 (p0) outliers start: 45 outliers final: 29 residues processed: 299 average time/residue: 0.1549 time to fit residues: 66.6433 Evaluate side-chains 299 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 42 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 198 optimal weight: 0.0770 chunk 156 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS C 329 HIS D 42 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 = 0.3907 r_free = 0.3907 target = 0.172892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128669 restraints weight = 19387.642| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.97 r_work: 0.3132 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2646 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= 0.122 Angle : 0.524 9.044 24005 Z= 0.261 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.045 3125 Dihedral : 7.832 124.554 2617 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 10.05 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2228 helix: 1.77 (0.17), residues: 929 sheet: 0.44 (0.30), residues: 324 loop : -0.66 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 36 TYR 0.022 0.001 TYR A 225 PHE 0.011 0.001 PHE C 347 TRP 0.005 0.001 TRP E 238 HIS 0.004 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00287 (17775) covalent geometry : angle 0.51968 (23993) hydrogen bonds : bond 0.03043 ( 804) hydrogen bonds : angle 4.18488 ( 2319) metal coordination : bond 0.00373 ( 8) metal coordination : angle 3.03153 ( 12) Misc. bond : bond 0.00017 ( 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 316 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5274 (t) cc_final: 0.5047 (p) REVERT: A 95 TYR cc_start: 0.8787 (t80) cc_final: 0.8317 (t80) REVERT: A 151 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7826 (tt0) REVERT: A 154 LYS cc_start: 0.8506 (mptt) cc_final: 0.8116 (mmtt) REVERT: A 216 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8428 (mmtm) REVERT: A 293 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6559 (t0) REVERT: C 87 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8201 (mt-10) REVERT: C 108 GLU cc_start: 0.8435 (pt0) cc_final: 0.7844 (pm20) REVERT: C 197 MET cc_start: 0.5885 (ttm) cc_final: 0.5641 (tpt) REVERT: C 203 TYR cc_start: 0.6211 (t80) cc_final: 0.5857 (t80) REVERT: C 280 GLU cc_start: 0.7807 (tt0) cc_final: 0.7583 (tt0) REVERT: C 331 ARG cc_start: 0.7911 (ttt-90) cc_final: 0.7379 (ttp80) REVERT: C 429 ASN cc_start: 0.7618 (m-40) cc_final: 0.7092 (m-40) REVERT: D 118 MET cc_start: 0.8445 (ptp) cc_final: 0.8181 (ptt) REVERT: D 274 LEU cc_start: 0.8930 (mt) cc_final: 0.8680 (mt) REVERT: D 278 MET cc_start: 0.8347 (mmm) cc_final: 0.8102 (mmm) REVERT: E 50 LEU cc_start: 0.7806 (tp) cc_final: 0.7568 (tp) REVERT: E 65 GLN cc_start: 0.8114 (mt0) cc_final: 0.7831 (mt0) REVERT: E 128 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8482 (mp) REVERT: E 154 LYS cc_start: 0.8878 (mptt) cc_final: 0.8504 (mmtt) REVERT: E 188 MET cc_start: 0.8977 (ttm) cc_final: 0.8713 (ttt) REVERT: E 219 MET cc_start: 0.8371 (ttm) cc_final: 0.8009 (mtp) REVERT: E 307 ASN cc_start: 0.8521 (m-40) cc_final: 0.8309 (m110) REVERT: F 123 MET cc_start: 0.6841 (mtp) cc_final: 0.6477 (mtt) REVERT: G 27 LYS cc_start: 0.8615 (mttt) cc_final: 0.8404 (mtmt) REVERT: G 97 ARG cc_start: 0.7346 (mtt90) cc_final: 0.6896 (mtm110) REVERT: G 184 MET cc_start: 0.7616 (tmm) cc_final: 0.7175 (tmm) REVERT: G 239 VAL cc_start: 0.8897 (t) cc_final: 0.8675 (m) REVERT: G 258 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7139 (mm-30) REVERT: G 288 GLU cc_start: 0.7542 (pt0) cc_final: 0.7292 (pt0) REVERT: G 324 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7648 (mptt) REVERT: G 408 GLU cc_start: 0.8690 (tt0) cc_final: 0.8399 (mt-10) REVERT: H 62 HIS cc_start: 0.8176 (m90) cc_final: 0.7925 (m-70) REVERT: H 84 LYS cc_start: 0.6306 (mmtt) cc_final: 0.5913 (mtpt) REVERT: H 111 MET cc_start: 0.8827 (mtp) cc_final: 0.8589 (mtp) REVERT: H 153 ASN cc_start: 0.7664 (p0) cc_final: 0.7021 (p0) outliers start: 39 outliers final: 28 residues processed: 296 average time/residue: 0.1440 time to fit residues: 62.2540 Evaluate side-chains 299 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 118 MET 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 28 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 189 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS C 329 HIS D 42 ASN F 126 GLN H 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.171907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128825 restraints weight = 19306.989| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.96 r_work: 0.3205 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17785 Z= 0.142 Angle : 0.540 9.214 24005 Z= 0.268 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.045 3125 Dihedral : 7.748 119.733 2617 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.03 % Allowed : 10.71 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.18), residues: 2228 helix: 1.72 (0.17), residues: 930 sheet: 0.29 (0.31), residues: 322 loop : -0.71 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 41 TYR 0.022 0.001 TYR A 225 PHE 0.013 0.001 PHE G 277 TRP 0.005 0.001 TRP E 238 HIS 0.004 0.001 HIS G 297 Details of bonding type rmsd covalent geometry : bond 0.00342 (17775) covalent geometry : angle 0.53564 (23993) hydrogen bonds : bond 0.03146 ( 804) hydrogen bonds : angle 4.20903 ( 2319) metal coordination : bond 0.00349 ( 8) metal coordination : angle 3.24031 ( 12) Misc. bond : bond 0.00043 ( 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 304 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5263 (t) cc_final: 0.5044 (p) REVERT: A 95 TYR cc_start: 0.8836 (t80) cc_final: 0.8329 (t80) REVERT: A 151 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7760 (tt0) REVERT: A 154 LYS cc_start: 0.8498 (mptt) cc_final: 0.8107 (mmtt) REVERT: A 216 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8412 (mmtm) REVERT: A 261 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7247 (tt) REVERT: A 293 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6738 (t0) REVERT: C 87 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8169 (mt-10) REVERT: C 108 GLU cc_start: 0.8411 (pt0) cc_final: 0.7814 (pm20) REVERT: C 184 MET cc_start: 0.6757 (ppp) cc_final: 0.6459 (mtp) REVERT: C 197 MET cc_start: 0.5930 (ttm) cc_final: 0.5637 (tpt) REVERT: C 280 GLU cc_start: 0.7855 (tt0) cc_final: 0.7615 (tt0) REVERT: C 429 ASN cc_start: 0.7601 (m-40) cc_final: 0.7066 (m-40) REVERT: D 34 LEU cc_start: 0.8944 (mt) cc_final: 0.8624 (mp) REVERT: D 118 MET cc_start: 0.8530 (ptp) cc_final: 0.8264 (ptt) REVERT: D 274 LEU cc_start: 0.8892 (mt) cc_final: 0.8646 (mt) REVERT: D 278 MET cc_start: 0.8362 (mmm) cc_final: 0.8110 (mmm) REVERT: E 50 LEU cc_start: 0.7784 (tp) cc_final: 0.7555 (tp) REVERT: E 65 GLN cc_start: 0.8068 (mt0) cc_final: 0.7737 (mt0) REVERT: E 128 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8479 (mp) REVERT: E 154 LYS cc_start: 0.8850 (mptt) cc_final: 0.8470 (mmtt) REVERT: E 188 MET cc_start: 0.9024 (ttm) cc_final: 0.8738 (ttt) REVERT: E 219 MET cc_start: 0.8398 (ttm) cc_final: 0.8036 (mtp) REVERT: E 307 ASN cc_start: 0.8457 (m-40) cc_final: 0.8250 (m110) REVERT: F 123 MET cc_start: 0.6809 (mtp) cc_final: 0.6433 (mtt) REVERT: F 126 GLN cc_start: 0.7896 (mt0) cc_final: 0.7683 (mt0) REVERT: G 15 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8475 (tt) REVERT: G 97 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6946 (mtm110) REVERT: G 184 MET cc_start: 0.7614 (tmm) cc_final: 0.7169 (tmm) REVERT: G 258 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7005 (mm-30) REVERT: G 288 GLU cc_start: 0.7500 (pt0) cc_final: 0.7195 (pt0) REVERT: G 324 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7559 (mptt) REVERT: H 62 HIS cc_start: 0.8028 (m90) cc_final: 0.7758 (m-70) REVERT: H 84 LYS cc_start: 0.6308 (mmtt) cc_final: 0.5909 (mtpt) REVERT: H 111 MET cc_start: 0.8834 (mtp) cc_final: 0.8605 (mtp) REVERT: H 153 ASN cc_start: 0.7654 (p0) cc_final: 0.7001 (p0) outliers start: 37 outliers final: 28 residues processed: 285 average time/residue: 0.1494 time to fit residues: 61.3484 Evaluate side-chains 296 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 195 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS D 42 ASN G 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.172548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129372 restraints weight = 19336.825| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2847 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= 0.121 Angle : 0.528 9.618 24005 Z= 0.262 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.044 3125 Dihedral : 7.576 117.330 2617 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.87 % Allowed : 11.43 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2228 helix: 1.77 (0.17), residues: 930 sheet: 0.29 (0.30), residues: 322 loop : -0.67 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 129 TYR 0.022 0.001 TYR G 439 PHE 0.011 0.001 PHE G 277 TRP 0.005 0.001 TRP E 238 HIS 0.004 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00287 (17775) covalent geometry : angle 0.52332 (23993) hydrogen bonds : bond 0.02958 ( 804) hydrogen bonds : angle 4.13596 ( 2319) metal coordination : bond 0.00329 ( 8) metal coordination : angle 3.23329 ( 12) Misc. bond : bond 0.00023 ( 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 305 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5284 (t) cc_final: 0.5067 (p) REVERT: A 95 TYR cc_start: 0.8777 (t80) cc_final: 0.8281 (t80) REVERT: A 151 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7690 (tt0) REVERT: A 154 LYS cc_start: 0.8518 (mptt) cc_final: 0.8149 (mmtt) REVERT: A 216 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8466 (mmtm) REVERT: A 261 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 293 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6849 (t0) REVERT: C 87 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8163 (mt-10) REVERT: C 108 GLU cc_start: 0.8416 (pt0) cc_final: 0.7849 (pm20) REVERT: C 184 MET cc_start: 0.6864 (ppp) cc_final: 0.6608 (mtp) REVERT: C 197 MET cc_start: 0.5973 (ttm) cc_final: 0.5678 (tpt) REVERT: C 280 GLU cc_start: 0.7868 (tt0) cc_final: 0.7659 (tt0) REVERT: C 429 ASN cc_start: 0.7619 (m-40) cc_final: 0.6947 (m-40) REVERT: D 274 LEU cc_start: 0.8939 (mt) cc_final: 0.8684 (mt) REVERT: D 278 MET cc_start: 0.8369 (mmm) cc_final: 0.8137 (mmm) REVERT: E 50 LEU cc_start: 0.7825 (tp) cc_final: 0.7586 (tp) REVERT: E 65 GLN cc_start: 0.8133 (mt0) cc_final: 0.7821 (mt0) REVERT: E 128 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8456 (mp) REVERT: E 154 LYS cc_start: 0.8868 (mptt) cc_final: 0.8497 (mmtt) REVERT: E 188 MET cc_start: 0.8989 (ttm) cc_final: 0.8734 (ttt) REVERT: E 219 MET cc_start: 0.8399 (ttm) cc_final: 0.8028 (mtp) REVERT: F 123 MET cc_start: 0.6838 (mtp) cc_final: 0.6490 (mtt) REVERT: G 97 ARG cc_start: 0.7381 (mtt90) cc_final: 0.7058 (mtm110) REVERT: G 184 MET cc_start: 0.7615 (tmm) cc_final: 0.7174 (tmm) REVERT: G 258 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7118 (mm-30) REVERT: G 288 GLU cc_start: 0.7559 (pt0) cc_final: 0.7250 (pt0) REVERT: G 324 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7558 (mptt) REVERT: H 62 HIS cc_start: 0.8036 (m90) cc_final: 0.7805 (m-70) REVERT: H 84 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5913 (mtpt) REVERT: H 111 MET cc_start: 0.8845 (mtp) cc_final: 0.8626 (mtp) REVERT: H 153 ASN cc_start: 0.7671 (p0) cc_final: 0.7031 (p0) outliers start: 34 outliers final: 26 residues processed: 288 average time/residue: 0.1530 time to fit residues: 63.1074 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 : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS D 42 ASN F 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.169413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125948 restraints weight = 19472.385| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.97 r_work: 0.3172 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17785 Z= 0.195 Angle : 0.586 6.827 24005 Z= 0.293 Chirality : 0.046 0.234 2660 Planarity : 0.004 0.043 3125 Dihedral : 7.575 117.838 2617 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.87 % Allowed : 11.65 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2228 helix: 1.54 (0.17), residues: 930 sheet: 0.34 (0.31), residues: 310 loop : -0.78 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 36 TYR 0.025 0.002 TYR A 225 PHE 0.016 0.002 PHE G 277 TRP 0.006 0.001 TRP D 24 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00477 (17775) covalent geometry : angle 0.58235 (23993) hydrogen bonds : bond 0.03540 ( 804) hydrogen bonds : angle 4.31853 ( 2319) metal coordination : bond 0.00535 ( 8) metal coordination : angle 3.15904 ( 12) Misc. bond : bond 0.00050 ( 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 307 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5293 (t) cc_final: 0.5070 (p) REVERT: A 95 TYR cc_start: 0.8884 (t80) cc_final: 0.8332 (t80) REVERT: A 154 LYS cc_start: 0.8581 (mptt) cc_final: 0.8219 (mmtt) REVERT: A 216 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8403 (mmtm) REVERT: A 261 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7350 (tt) REVERT: A 293 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6807 (t0) REVERT: C 87 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8162 (mt-10) REVERT: C 184 MET cc_start: 0.6788 (ppp) cc_final: 0.6505 (mtp) REVERT: C 197 MET cc_start: 0.5950 (ttm) cc_final: 0.5699 (tpt) REVERT: C 436 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6828 (m-40) REVERT: D 274 LEU cc_start: 0.8963 (mt) cc_final: 0.8706 (mt) REVERT: E 50 LEU cc_start: 0.7811 (tp) cc_final: 0.7584 (tp) REVERT: E 65 GLN cc_start: 0.8113 (mt0) cc_final: 0.7847 (mt0) REVERT: E 128 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8469 (mp) REVERT: E 154 LYS cc_start: 0.8843 (mptt) cc_final: 0.8482 (mmtt) REVERT: E 219 MET cc_start: 0.8459 (ttm) cc_final: 0.8160 (mtp) REVERT: E 265 ASP cc_start: 0.8128 (m-30) cc_final: 0.7686 (t0) REVERT: F 123 MET cc_start: 0.7182 (mtp) cc_final: 0.6780 (mtt) REVERT: G 97 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6850 (mtm110) REVERT: G 184 MET cc_start: 0.7602 (tmm) cc_final: 0.7170 (tmm) REVERT: G 258 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7085 (mm-30) REVERT: G 283 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7523 (mm-30) REVERT: G 288 GLU cc_start: 0.7501 (pt0) cc_final: 0.7186 (pt0) REVERT: G 324 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7497 (mptt) REVERT: H 41 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7371 (mpt180) REVERT: H 62 HIS cc_start: 0.8075 (m90) cc_final: 0.7814 (m-70) REVERT: H 111 MET cc_start: 0.8875 (mtp) cc_final: 0.8630 (mtp) REVERT: H 153 ASN cc_start: 0.7765 (p0) cc_final: 0.7064 (p0) outliers start: 34 outliers final: 28 residues processed: 291 average time/residue: 0.1699 time to fit residues: 71.0073 Evaluate side-chains 299 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 78 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS D 42 ASN E 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128675 restraints weight = 19227.589| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.99 r_work: 0.3205 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3038 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= 0.120 Angle : 0.536 7.675 24005 Z= 0.267 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.043 3125 Dihedral : 7.378 113.855 2617 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.32 % Allowed : 12.69 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2228 helix: 1.70 (0.17), residues: 931 sheet: 0.06 (0.31), residues: 302 loop : -0.68 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 36 TYR 0.024 0.001 TYR A 225 PHE 0.012 0.001 PHE G 430 TRP 0.005 0.001 TRP E 238 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00282 (17775) covalent geometry : angle 0.53106 (23993) hydrogen bonds : bond 0.02960 ( 804) hydrogen bonds : angle 4.18132 ( 2319) metal coordination : bond 0.00363 ( 8) metal coordination : angle 3.31537 ( 12) Misc. bond : bond 0.00022 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5236 (t) cc_final: 0.5023 (p) REVERT: A 95 TYR cc_start: 0.8778 (t80) cc_final: 0.8223 (t80) REVERT: A 154 LYS cc_start: 0.8484 (mptt) cc_final: 0.8141 (mmtt) REVERT: A 216 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8460 (mmtm) REVERT: A 293 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6854 (t0) REVERT: C 108 GLU cc_start: 0.8377 (pt0) cc_final: 0.7779 (pm20) REVERT: C 184 MET cc_start: 0.6833 (ppp) cc_final: 0.6539 (mtp) REVERT: C 197 MET cc_start: 0.5965 (ttm) cc_final: 0.5658 (tpt) REVERT: D 274 LEU cc_start: 0.8888 (mt) cc_final: 0.8634 (mt) REVERT: D 278 MET cc_start: 0.8337 (mmm) cc_final: 0.8085 (mmm) REVERT: E 50 LEU cc_start: 0.7766 (tp) cc_final: 0.7543 (tp) REVERT: E 65 GLN cc_start: 0.8071 (mt0) cc_final: 0.7757 (mt0) REVERT: E 128 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8433 (mp) REVERT: E 154 LYS cc_start: 0.8841 (mptt) cc_final: 0.8442 (mmtt) REVERT: E 188 MET cc_start: 0.9029 (ttm) cc_final: 0.8768 (ttt) REVERT: E 219 MET cc_start: 0.8419 (ttm) cc_final: 0.7990 (mtp) REVERT: F 123 MET cc_start: 0.6731 (mtp) cc_final: 0.6358 (mtt) REVERT: G 38 ASP cc_start: 0.8237 (t0) cc_final: 0.7970 (t0) REVERT: G 97 ARG cc_start: 0.7319 (mtt90) cc_final: 0.7026 (mtm110) REVERT: G 184 MET cc_start: 0.7617 (tmm) cc_final: 0.7175 (tmm) REVERT: G 258 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7067 (mm-30) REVERT: G 288 GLU cc_start: 0.7520 (pt0) cc_final: 0.7190 (pt0) REVERT: G 324 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7447 (mptt) REVERT: H 41 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7311 (mpt180) REVERT: H 62 HIS cc_start: 0.7834 (m90) cc_final: 0.7598 (m-70) REVERT: H 111 MET cc_start: 0.8843 (mtp) cc_final: 0.8620 (mtp) REVERT: H 153 ASN cc_start: 0.7689 (p0) cc_final: 0.7023 (p0) outliers start: 24 outliers final: 18 residues processed: 284 average time/residue: 0.1697 time to fit residues: 69.3623 Evaluate side-chains 289 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain H residue 118 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 178 optimal weight: 0.0870 chunk 198 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 chunk 78 optimal weight: 0.9980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.173062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130042 restraints weight = 19390.762| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.01 r_work: 0.3218 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17785 Z= 0.108 Angle : 0.527 7.478 24005 Z= 0.262 Chirality : 0.044 0.234 2660 Planarity : 0.004 0.043 3125 Dihedral : 7.309 107.099 2617 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.32 % Allowed : 12.53 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2228 helix: 1.80 (0.17), residues: 931 sheet: 0.19 (0.30), residues: 322 loop : -0.62 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 36 TYR 0.020 0.001 TYR A 225 PHE 0.011 0.001 PHE G 430 TRP 0.004 0.001 TRP C 367 HIS 0.003 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00250 (17775) covalent geometry : angle 0.52223 (23993) hydrogen bonds : bond 0.02829 ( 804) hydrogen bonds : angle 4.10002 ( 2319) metal coordination : bond 0.00303 ( 8) metal coordination : angle 3.12162 ( 12) Misc. bond : bond 0.00050 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5334.53 seconds wall clock time: 91 minutes 51.05 seconds (5511.05 seconds total)