Starting phenix.real_space_refine on Sun Jun 15 14:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxz_42790/06_2025/8uxz_42790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxz_42790/06_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_42790/06_2025/8uxz_42790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxz_42790/06_2025/8uxz_42790.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxz_42790/06_2025/8uxz_42790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxz_42790/06_2025/8uxz_42790_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17474 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2452 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 584 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "C" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3433 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 424} Chain: "D" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2173 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 267} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2452 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 299} Chain: "F" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 584 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "G" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3433 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 424} Chain: "H" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2006 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6679 SG CYS D 27 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: 10.78, per 1000 atoms: 0.62 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: 4.32 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.19 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: 6.10 Time building geometry restraints manager: 5.08 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 285 or resid 301 through 302)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.210 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.005 0.001 TRP I 3 HIS 0.004 0.001 HIS E 118 PHE 0.011 0.001 PHE D 125 TYR 0.017 0.001 TYR E 225 ARG 0.005 0.001 ARG E 309 Details of bonding type rmsd hydrogen bonds : bond 0.16527 ( 804) hydrogen bonds : angle 6.53370 ( 2319) metal coordination : bond 0.00380 ( 8) metal coordination : angle 2.26609 ( 12) covalent geometry : bond 0.00361 (17775) covalent geometry : angle 0.56606 (23993) 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 : 1.775 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: 0.8561 (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: 0.6061 (p) REVERT: F 123 MET cc_start: 0.6909 (mtp) cc_final: 0.6555 (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 159 LYS cc_start: 0.6229 (mtpt) cc_final: 0.5912 (mtmm) REVERT: G 258 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6741 (mm-30) REVERT: G 286 PHE cc_start: 0.8262 (t80) cc_final: 0.7151 (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: 0.7389 (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: 0.3650 time to fit residues: 210.0290 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 : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.0570 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 0.2980 chunk 128 optimal weight: 0.0570 chunk 199 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 C 329 HIS G 94 GLN H 153 ASN H 176 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133423 restraints weight = 19245.846| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.99 r_work: 0.3234 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1690 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= 0.125 Angle : 0.554 7.944 24005 Z= 0.283 Chirality : 0.045 0.248 2660 Planarity : 0.004 0.043 3125 Dihedral : 8.879 125.334 2617 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.10 % Allowed : 7.09 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2228 helix: 1.71 (0.18), residues: 917 sheet: 0.54 (0.30), residues: 314 loop : -0.56 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 61 HIS 0.004 0.001 HIS C 297 PHE 0.018 0.001 PHE E 8 TYR 0.019 0.001 TYR H 35 ARG 0.008 0.001 ARG G 170 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 804) hydrogen bonds : angle 4.84884 ( 2319) metal coordination : bond 0.00357 ( 8) metal coordination : angle 1.72666 ( 12) covalent geometry : bond 0.00275 (17775) covalent geometry : angle 0.55321 (23993) Misc. bond : bond 0.00502 ( 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 312 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8912 (t80) cc_final: 0.8579 (t80) REVERT: A 151 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7848 (tt0) REVERT: A 154 LYS cc_start: 0.8582 (mptt) cc_final: 0.8270 (mmpt) REVERT: A 216 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8206 (mmtm) REVERT: A 293 ASP cc_start: 0.7313 (m-30) cc_final: 0.7075 (t0) REVERT: C 87 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8253 (mt-10) REVERT: C 197 MET cc_start: 0.5957 (ttm) cc_final: 0.5609 (tpt) REVERT: C 203 TYR cc_start: 0.6431 (t80) cc_final: 0.5893 (t80) REVERT: C 232 MET cc_start: 0.8678 (mmt) cc_final: 0.8442 (tpp) REVERT: C 280 GLU cc_start: 0.7519 (tt0) cc_final: 0.7207 (tt0) REVERT: C 331 ARG cc_start: 0.8064 (ttt-90) cc_final: 0.7509 (ttp80) REVERT: D 177 MET cc_start: 0.8307 (mtp) cc_final: 0.8043 (mtp) REVERT: D 274 LEU cc_start: 0.8912 (mt) cc_final: 0.8659 (mt) REVERT: D 278 MET cc_start: 0.8275 (mmm) cc_final: 0.8059 (mmm) REVERT: E 50 LEU cc_start: 0.7739 (tp) cc_final: 0.7507 (tp) REVERT: E 154 LYS cc_start: 0.8883 (mptt) cc_final: 0.8499 (mmtt) REVERT: E 219 MET cc_start: 0.8124 (ttm) cc_final: 0.7835 (ttm) REVERT: E 271 PRO cc_start: 0.8444 (Cg_exo) cc_final: 0.8155 (Cg_endo) REVERT: F 123 MET cc_start: 0.6832 (mtp) cc_final: 0.6519 (mtt) REVERT: G 23 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6771 (mt-10) REVERT: G 27 LYS cc_start: 0.8578 (mttt) cc_final: 0.8324 (mtmt) REVERT: G 159 LYS cc_start: 0.7507 (mtpt) cc_final: 0.6802 (mtmm) REVERT: G 184 MET cc_start: 0.7520 (tmm) cc_final: 0.7248 (tmm) REVERT: G 239 VAL cc_start: 0.8900 (t) cc_final: 0.8667 (m) REVERT: G 258 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7172 (mm-30) REVERT: G 286 PHE cc_start: 0.8537 (t80) cc_final: 0.7481 (t80) REVERT: G 324 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7654 (mptt) REVERT: H 84 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5895 (mtpt) REVERT: H 175 MET cc_start: 0.8732 (mmt) cc_final: 0.8365 (mmt) REVERT: H 186 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7411 (tptt) outliers start: 20 outliers final: 12 residues processed: 301 average time/residue: 0.4270 time to fit residues: 185.9976 Evaluate side-chains 274 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 262 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 235 GLN 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 5 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.172646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129166 restraints weight = 19337.518| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.99 r_work: 0.3178 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17785 Z= 0.167 Angle : 0.571 11.245 24005 Z= 0.286 Chirality : 0.045 0.236 2660 Planarity : 0.004 0.045 3125 Dihedral : 8.538 119.003 2617 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.87 % Allowed : 7.86 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2228 helix: 1.63 (0.17), residues: 927 sheet: 0.75 (0.32), residues: 292 loop : -0.70 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 24 HIS 0.005 0.001 HIS H 62 PHE 0.014 0.002 PHE E 8 TYR 0.027 0.002 TYR E 225 ARG 0.008 0.001 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 804) hydrogen bonds : angle 4.55554 ( 2319) metal coordination : bond 0.00712 ( 8) metal coordination : angle 4.05590 ( 12) covalent geometry : bond 0.00402 (17775) covalent geometry : angle 0.56398 (23993) Misc. bond : bond 0.00174 ( 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 316 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5333 (t) cc_final: 0.5089 (p) REVERT: A 95 TYR cc_start: 0.8880 (t80) cc_final: 0.8387 (t80) REVERT: A 151 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7855 (tt0) REVERT: A 154 LYS cc_start: 0.8516 (mptt) cc_final: 0.8140 (mmtt) REVERT: A 216 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8179 (mmtm) REVERT: A 293 ASP cc_start: 0.7279 (m-30) cc_final: 0.6921 (t0) REVERT: C 87 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 197 MET cc_start: 0.5914 (ttm) cc_final: 0.5548 (tpt) REVERT: C 203 TYR cc_start: 0.6583 (t80) cc_final: 0.5974 (t80) REVERT: C 232 MET cc_start: 0.8553 (mmt) cc_final: 0.8286 (tpp) REVERT: C 280 GLU cc_start: 0.7664 (tt0) cc_final: 0.7306 (tt0) REVERT: C 331 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7522 (ttp80) REVERT: C 429 ASN cc_start: 0.7624 (m-40) cc_final: 0.7240 (m-40) REVERT: D 274 LEU cc_start: 0.8961 (mt) cc_final: 0.8729 (mt) REVERT: D 278 MET cc_start: 0.8393 (mmm) cc_final: 0.8137 (mmm) REVERT: E 50 LEU cc_start: 0.7723 (tp) cc_final: 0.7488 (tp) REVERT: E 65 GLN cc_start: 0.8131 (mt0) cc_final: 0.7832 (mt0) REVERT: E 154 LYS cc_start: 0.8876 (mptt) cc_final: 0.8520 (mmtt) REVERT: F 123 MET cc_start: 0.6890 (mtp) cc_final: 0.6589 (mtt) REVERT: G 23 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7014 (mt-10) REVERT: G 27 LYS cc_start: 0.8619 (mttt) cc_final: 0.8393 (mtmt) REVERT: G 184 MET cc_start: 0.7792 (tmm) cc_final: 0.7454 (tmm) REVERT: G 239 VAL cc_start: 0.8953 (t) cc_final: 0.8690 (m) REVERT: G 258 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7108 (mm-30) REVERT: G 324 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7648 (mptt) REVERT: H 84 LYS cc_start: 0.6366 (mmtt) cc_final: 0.6004 (mtpt) REVERT: H 111 MET cc_start: 0.8787 (mtp) cc_final: 0.8553 (mtp) REVERT: H 153 ASN cc_start: 0.7377 (p0) cc_final: 0.6792 (p0) REVERT: H 186 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7445 (tptt) outliers start: 34 outliers final: 26 residues processed: 297 average time/residue: 0.3831 time to fit residues: 163.0762 Evaluate side-chains 289 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 VAL 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 97 ARG 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 78 GLU 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 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 7 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 216 optimal weight: 0.0970 chunk 52 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 81 HIS C 329 HIS ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 421 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 = 0.3889 r_free = 0.3889 target = 0.170678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126850 restraints weight = 19313.555| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.96 r_work: 0.3121 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17785 Z= 0.185 Angle : 0.578 8.813 24005 Z= 0.290 Chirality : 0.046 0.235 2660 Planarity : 0.004 0.045 3125 Dihedral : 8.374 127.550 2617 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 9.01 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2228 helix: 1.50 (0.17), residues: 928 sheet: 0.56 (0.32), residues: 272 loop : -0.82 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 24 HIS 0.005 0.001 HIS H 62 PHE 0.023 0.002 PHE G 286 TYR 0.026 0.002 TYR A 225 ARG 0.007 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 804) hydrogen bonds : angle 4.48691 ( 2319) metal coordination : bond 0.00628 ( 8) metal coordination : angle 3.13292 ( 12) covalent geometry : bond 0.00448 (17775) covalent geometry : angle 0.57419 (23993) Misc. bond : bond 0.00032 ( 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 314 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5258 (t) cc_final: 0.5036 (p) REVERT: A 95 TYR cc_start: 0.8876 (t80) cc_final: 0.8388 (t80) REVERT: A 151 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7780 (tt0) REVERT: A 154 LYS cc_start: 0.8536 (mptt) cc_final: 0.8135 (mmtt) REVERT: A 216 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8217 (mmtm) REVERT: A 261 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6959 (tt) REVERT: C 87 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 197 MET cc_start: 0.5951 (ttm) cc_final: 0.5746 (tpt) REVERT: C 232 MET cc_start: 0.8581 (mmt) cc_final: 0.8303 (tpp) REVERT: C 280 GLU cc_start: 0.7875 (tt0) cc_final: 0.7543 (tt0) REVERT: C 331 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7510 (ttp80) REVERT: C 384 MET cc_start: 0.8747 (ttt) cc_final: 0.8521 (ttt) REVERT: C 429 ASN cc_start: 0.7713 (m-40) cc_final: 0.7140 (m-40) REVERT: D 274 LEU cc_start: 0.8965 (mt) cc_final: 0.8731 (mt) REVERT: E 50 LEU cc_start: 0.7786 (tp) cc_final: 0.7545 (tp) REVERT: E 65 GLN cc_start: 0.8198 (mt0) cc_final: 0.7915 (mt0) REVERT: E 128 ILE cc_start: 0.8727 (mp) cc_final: 0.8462 (mp) REVERT: E 154 LYS cc_start: 0.8862 (mptt) cc_final: 0.8485 (mmtt) REVERT: E 307 ASN cc_start: 0.8462 (m-40) cc_final: 0.8245 (m110) REVERT: F 123 MET cc_start: 0.6862 (mtp) cc_final: 0.6493 (mtt) REVERT: F 126 GLN cc_start: 0.7719 (mt0) cc_final: 0.7442 (mt0) REVERT: G 15 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8552 (tt) REVERT: G 23 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7117 (mt-10) REVERT: G 27 LYS cc_start: 0.8610 (mttt) cc_final: 0.8361 (mtmt) REVERT: G 184 MET cc_start: 0.7721 (tmm) cc_final: 0.7357 (tmm) REVERT: G 239 VAL cc_start: 0.8941 (t) cc_final: 0.8690 (m) REVERT: G 258 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7128 (mm-30) REVERT: G 288 GLU cc_start: 0.7525 (pt0) cc_final: 0.7269 (pt0) REVERT: G 324 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7562 (mptt) REVERT: G 408 GLU cc_start: 0.8792 (tt0) cc_final: 0.8527 (mt-10) REVERT: H 111 MET cc_start: 0.8834 (mtp) cc_final: 0.8591 (mtp) REVERT: H 153 ASN cc_start: 0.7826 (p0) cc_final: 0.7140 (p0) outliers start: 38 outliers final: 25 residues processed: 292 average time/residue: 0.3398 time to fit residues: 142.2584 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 : 1.922 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain A residue 242 ASP 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 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 235 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 315 SER 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 131 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.170682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127124 restraints weight = 19503.155| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.96 r_work: 0.3122 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17785 Z= 0.164 Angle : 0.557 8.544 24005 Z= 0.278 Chirality : 0.045 0.235 2660 Planarity : 0.004 0.045 3125 Dihedral : 8.191 130.175 2617 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.53 % Allowed : 9.40 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2228 helix: 1.53 (0.17), residues: 929 sheet: 0.43 (0.32), residues: 282 loop : -0.82 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 238 HIS 0.004 0.001 HIS A 118 PHE 0.013 0.001 PHE C 277 TYR 0.024 0.001 TYR A 225 ARG 0.006 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 804) hydrogen bonds : angle 4.38657 ( 2319) metal coordination : bond 0.00521 ( 8) metal coordination : angle 3.26699 ( 12) covalent geometry : bond 0.00398 (17775) covalent geometry : angle 0.55219 (23993) Misc. bond : bond 0.00028 ( 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: 46 poor density : 277 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5240 (t) cc_final: 0.5020 (p) REVERT: A 95 TYR cc_start: 0.8854 (t80) cc_final: 0.8365 (t80) REVERT: A 151 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7804 (tt0) REVERT: A 154 LYS cc_start: 0.8535 (mptt) cc_final: 0.8136 (mmtt) REVERT: A 216 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8000 (mmtm) REVERT: A 261 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7090 (tt) REVERT: A 293 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6730 (t0) REVERT: C 87 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8199 (mt-10) REVERT: C 203 TYR cc_start: 0.6279 (t80) cc_final: 0.5919 (t80) REVERT: C 232 MET cc_start: 0.8537 (mmt) cc_final: 0.8306 (tpp) REVERT: C 280 GLU cc_start: 0.7890 (tt0) cc_final: 0.7621 (tt0) REVERT: C 429 ASN cc_start: 0.7608 (m-40) cc_final: 0.7093 (m-40) REVERT: C 436 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6627 (m-40) REVERT: D 118 MET cc_start: 0.8523 (ptp) cc_final: 0.8249 (ptt) REVERT: D 274 LEU cc_start: 0.8971 (mt) cc_final: 0.8730 (mt) REVERT: E 50 LEU cc_start: 0.7815 (tp) cc_final: 0.7563 (tp) REVERT: E 65 GLN cc_start: 0.8180 (mt0) cc_final: 0.7880 (mt0) REVERT: E 128 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8431 (mp) REVERT: E 154 LYS cc_start: 0.8856 (mptt) cc_final: 0.8482 (mmtt) REVERT: E 307 ASN cc_start: 0.8457 (m-40) cc_final: 0.8250 (m110) REVERT: F 123 MET cc_start: 0.6860 (mtp) cc_final: 0.6491 (mtt) REVERT: G 15 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8536 (tt) REVERT: G 27 LYS cc_start: 0.8723 (mttt) cc_final: 0.8514 (mtmt) REVERT: G 97 ARG cc_start: 0.7012 (mtt90) cc_final: 0.6779 (mtm110) REVERT: G 184 MET cc_start: 0.7599 (tmm) cc_final: 0.7160 (tmm) REVERT: G 227 GLU cc_start: 0.7854 (pm20) cc_final: 0.7629 (pm20) REVERT: G 239 VAL cc_start: 0.8934 (t) cc_final: 0.8699 (m) REVERT: G 254 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7758 (ptm-80) REVERT: G 258 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7070 (mm-30) REVERT: G 288 GLU cc_start: 0.7552 (pt0) cc_final: 0.7246 (pt0) REVERT: G 324 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7642 (mptt) REVERT: H 62 HIS cc_start: 0.8186 (m90) cc_final: 0.7953 (m-70) REVERT: H 111 MET cc_start: 0.8854 (mtp) cc_final: 0.8619 (mtp) REVERT: H 153 ASN cc_start: 0.7821 (p0) cc_final: 0.7133 (p0) outliers start: 46 outliers final: 28 residues processed: 302 average time/residue: 0.3414 time to fit residues: 149.1419 Evaluate side-chains 290 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 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 235 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 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 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 296 ASP 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 G residue 437 ILE Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 151 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 198 optimal weight: 0.0570 chunk 19 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 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 = 0.172046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128675 restraints weight = 19411.123| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.98 r_work: 0.3168 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2753 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= 0.127 Angle : 0.533 8.764 24005 Z= 0.266 Chirality : 0.044 0.236 2660 Planarity : 0.004 0.045 3125 Dihedral : 7.955 129.357 2617 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.98 % Allowed : 11.26 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2228 helix: 1.62 (0.17), residues: 930 sheet: 0.40 (0.32), residues: 290 loop : -0.77 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 238 HIS 0.006 0.001 HIS D 62 PHE 0.011 0.001 PHE C 277 TYR 0.023 0.001 TYR A 225 ARG 0.007 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 804) hydrogen bonds : angle 4.25925 ( 2319) metal coordination : bond 0.00401 ( 8) metal coordination : angle 3.20632 ( 12) covalent geometry : bond 0.00299 (17775) covalent geometry : angle 0.52843 (23993) Misc. bond : bond 0.00019 ( 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 298 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5276 (t) cc_final: 0.5056 (p) REVERT: A 95 TYR cc_start: 0.8782 (t80) cc_final: 0.8294 (t80) REVERT: A 151 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7775 (tt0) REVERT: A 154 LYS cc_start: 0.8542 (mptt) cc_final: 0.8160 (mmtt) REVERT: A 216 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8402 (mmtm) REVERT: A 293 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6714 (t0) REVERT: C 87 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 184 MET cc_start: 0.6826 (ppp) cc_final: 0.6495 (mtp) REVERT: C 232 MET cc_start: 0.8549 (mmt) cc_final: 0.8305 (tpp) REVERT: C 280 GLU cc_start: 0.7892 (tt0) cc_final: 0.7653 (tt0) REVERT: C 384 MET cc_start: 0.8628 (ttt) cc_final: 0.8342 (ttt) REVERT: C 429 ASN cc_start: 0.7626 (m-40) cc_final: 0.7104 (m-40) REVERT: D 118 MET cc_start: 0.8481 (ptp) cc_final: 0.8207 (ptt) REVERT: D 274 LEU cc_start: 0.8890 (mt) cc_final: 0.8648 (mt) REVERT: D 278 MET cc_start: 0.8388 (mmm) cc_final: 0.8138 (mmm) REVERT: E 50 LEU cc_start: 0.7836 (tp) cc_final: 0.7594 (tp) REVERT: E 65 GLN cc_start: 0.8179 (mt0) cc_final: 0.7848 (mt0) REVERT: E 154 LYS cc_start: 0.8855 (mptt) cc_final: 0.8484 (mmtt) REVERT: F 123 MET cc_start: 0.6893 (mtp) cc_final: 0.6519 (mtt) REVERT: G 184 MET cc_start: 0.7604 (tmm) cc_final: 0.7174 (tmm) REVERT: G 254 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7826 (ptm-80) REVERT: G 258 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7076 (mm-30) REVERT: G 288 GLU cc_start: 0.7564 (pt0) cc_final: 0.7248 (pt0) REVERT: G 324 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7627 (mptt) REVERT: H 62 HIS cc_start: 0.8059 (m90) cc_final: 0.7806 (m-70) REVERT: H 84 LYS cc_start: 0.6164 (mmtt) cc_final: 0.5941 (mtpt) REVERT: H 111 MET cc_start: 0.8839 (mtp) cc_final: 0.8610 (mtp) REVERT: H 153 ASN cc_start: 0.7758 (p0) cc_final: 0.7062 (p0) outliers start: 36 outliers final: 22 residues processed: 281 average time/residue: 0.3381 time to fit residues: 140.0315 Evaluate side-chains 278 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 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 235 GLN 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 346 THR 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 125 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 0.1980 chunk 96 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 81 HIS C 329 HIS D 42 ASN G 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.171547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128214 restraints weight = 19203.207| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.96 r_work: 0.3203 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2843 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= 0.132 Angle : 0.537 9.389 24005 Z= 0.267 Chirality : 0.044 0.235 2660 Planarity : 0.004 0.045 3125 Dihedral : 7.796 124.008 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.20 % Allowed : 10.99 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2228 helix: 1.65 (0.17), residues: 930 sheet: 0.31 (0.31), residues: 304 loop : -0.72 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 238 HIS 0.004 0.001 HIS H 62 PHE 0.012 0.001 PHE G 277 TYR 0.022 0.001 TYR A 225 ARG 0.006 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 804) hydrogen bonds : angle 4.19656 ( 2319) metal coordination : bond 0.00395 ( 8) metal coordination : angle 3.05461 ( 12) covalent geometry : bond 0.00317 (17775) covalent geometry : angle 0.53242 (23993) Misc. bond : bond 0.00018 ( 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 302 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5253 (t) cc_final: 0.5040 (p) REVERT: A 95 TYR cc_start: 0.8839 (t80) cc_final: 0.8329 (t80) REVERT: A 151 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7724 (tt0) REVERT: A 154 LYS cc_start: 0.8512 (mptt) cc_final: 0.8107 (mmtt) REVERT: A 216 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8442 (mmtm) REVERT: A 293 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6763 (t0) REVERT: C 87 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8158 (mt-10) REVERT: C 232 MET cc_start: 0.8479 (mmt) cc_final: 0.8230 (tpp) REVERT: C 280 GLU cc_start: 0.7909 (tt0) cc_final: 0.7649 (tt0) REVERT: C 309 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8276 (mp) REVERT: C 429 ASN cc_start: 0.7588 (m-40) cc_final: 0.7057 (m-40) REVERT: D 118 MET cc_start: 0.8541 (ptp) cc_final: 0.8269 (ptt) REVERT: D 274 LEU cc_start: 0.8825 (mt) cc_final: 0.8582 (mt) REVERT: D 278 MET cc_start: 0.8345 (mmm) cc_final: 0.8083 (mmm) REVERT: E 50 LEU cc_start: 0.7779 (tp) cc_final: 0.7545 (tp) REVERT: E 65 GLN cc_start: 0.8104 (mt0) cc_final: 0.7776 (mt0) REVERT: E 128 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8448 (mp) REVERT: E 154 LYS cc_start: 0.8840 (mptt) cc_final: 0.8463 (mmtt) REVERT: E 307 ASN cc_start: 0.8235 (m110) cc_final: 0.8033 (m-40) REVERT: F 123 MET cc_start: 0.6815 (mtp) cc_final: 0.6445 (mtt) REVERT: G 184 MET cc_start: 0.7609 (tmm) cc_final: 0.7176 (tmm) REVERT: G 258 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7128 (mm-30) REVERT: G 288 GLU cc_start: 0.7510 (pt0) cc_final: 0.7183 (pt0) REVERT: G 324 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7502 (mptt) REVERT: G 442 LYS cc_start: 0.7891 (tmmt) cc_final: 0.7106 (mmtp) REVERT: G 443 LYS cc_start: 0.7414 (tttp) cc_final: 0.7148 (tttp) REVERT: H 62 HIS cc_start: 0.8042 (m90) cc_final: 0.7759 (m-70) REVERT: H 84 LYS cc_start: 0.6144 (mmtt) cc_final: 0.5907 (mtpt) REVERT: H 111 MET cc_start: 0.8816 (mtp) cc_final: 0.8598 (mtp) REVERT: H 153 ASN cc_start: 0.7710 (p0) cc_final: 0.7017 (p0) outliers start: 40 outliers final: 26 residues processed: 281 average time/residue: 0.4113 time to fit residues: 167.5392 Evaluate side-chains 286 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 ILE 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 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 188 MET Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 296 ASP 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 G residue 437 ILE 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 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 185 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 H 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128356 restraints weight = 19224.179| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.98 r_work: 0.3204 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2925 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= 0.127 Angle : 0.529 9.350 24005 Z= 0.263 Chirality : 0.044 0.235 2660 Planarity : 0.004 0.045 3125 Dihedral : 7.672 122.540 2617 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.87 % Allowed : 11.70 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2228 helix: 1.69 (0.17), residues: 930 sheet: 0.28 (0.30), residues: 322 loop : -0.71 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 238 HIS 0.004 0.001 HIS D 62 PHE 0.011 0.001 PHE G 277 TYR 0.021 0.001 TYR A 225 ARG 0.009 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 804) hydrogen bonds : angle 4.14892 ( 2319) metal coordination : bond 0.00359 ( 8) metal coordination : angle 3.00214 ( 12) covalent geometry : bond 0.00303 (17775) covalent geometry : angle 0.52464 (23993) Misc. bond : bond 0.00019 ( 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 300 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5262 (t) cc_final: 0.5040 (p) REVERT: A 95 TYR cc_start: 0.8782 (t80) cc_final: 0.8258 (t80) REVERT: A 151 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7728 (tt0) REVERT: A 154 LYS cc_start: 0.8498 (mptt) cc_final: 0.8119 (mmtt) REVERT: A 216 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8472 (mmtm) REVERT: A 293 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6779 (t0) REVERT: C 87 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 108 GLU cc_start: 0.8404 (pt0) cc_final: 0.7815 (pm20) REVERT: C 232 MET cc_start: 0.8487 (mmt) cc_final: 0.8249 (tpp) REVERT: C 280 GLU cc_start: 0.7919 (tt0) cc_final: 0.7677 (tt0) REVERT: C 429 ASN cc_start: 0.7672 (m-40) cc_final: 0.7156 (m-40) REVERT: C 436 ASN cc_start: 0.7039 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: D 274 LEU cc_start: 0.8829 (mt) cc_final: 0.8586 (mt) REVERT: D 278 MET cc_start: 0.8348 (mmm) cc_final: 0.8100 (mmm) REVERT: E 50 LEU cc_start: 0.7815 (tp) cc_final: 0.7589 (tp) REVERT: E 65 GLN cc_start: 0.8131 (mt0) cc_final: 0.7808 (mt0) REVERT: E 128 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8475 (mp) REVERT: E 154 LYS cc_start: 0.8806 (mptt) cc_final: 0.8455 (mmtt) REVERT: E 307 ASN cc_start: 0.8270 (m110) cc_final: 0.8038 (m-40) REVERT: F 123 MET cc_start: 0.6845 (mtp) cc_final: 0.6475 (mtt) REVERT: G 184 MET cc_start: 0.7607 (tmm) cc_final: 0.7178 (tmm) REVERT: G 211 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8602 (pt0) REVERT: G 258 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7145 (mm-30) REVERT: G 288 GLU cc_start: 0.7512 (pt0) cc_final: 0.7196 (pt0) REVERT: G 324 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7509 (mptt) REVERT: G 442 LYS cc_start: 0.7950 (tmmt) cc_final: 0.7093 (mmtp) REVERT: H 41 ARG cc_start: 0.7428 (mtt90) cc_final: 0.7044 (mpt180) REVERT: H 62 HIS cc_start: 0.7869 (m90) cc_final: 0.7621 (m-70) REVERT: H 84 LYS cc_start: 0.6143 (mmtt) cc_final: 0.5900 (mtpt) REVERT: H 111 MET cc_start: 0.8817 (mtp) cc_final: 0.8604 (mtp) REVERT: H 153 ASN cc_start: 0.7690 (p0) cc_final: 0.7012 (p0) outliers start: 34 outliers final: 27 residues processed: 282 average time/residue: 0.3285 time to fit residues: 133.8715 Evaluate side-chains 290 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 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 188 MET 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 211 GLU 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 G residue 437 ILE 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 163 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 218 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127396 restraints weight = 19408.245| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.96 r_work: 0.3190 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17785 Z= 0.147 Angle : 0.544 9.114 24005 Z= 0.271 Chirality : 0.045 0.234 2660 Planarity : 0.004 0.045 3125 Dihedral : 7.514 121.478 2617 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.87 % Allowed : 12.25 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2228 helix: 1.63 (0.17), residues: 930 sheet: 0.24 (0.30), residues: 322 loop : -0.73 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 238 HIS 0.004 0.001 HIS A 118 PHE 0.013 0.001 PHE G 277 TYR 0.023 0.001 TYR A 225 ARG 0.009 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 804) hydrogen bonds : angle 4.19064 ( 2319) metal coordination : bond 0.00375 ( 8) metal coordination : angle 3.20881 ( 12) covalent geometry : bond 0.00357 (17775) covalent geometry : angle 0.53948 (23993) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5256 (t) cc_final: 0.5038 (p) REVERT: A 95 TYR cc_start: 0.8846 (t80) cc_final: 0.8308 (t80) REVERT: A 151 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7724 (tt0) REVERT: A 154 LYS cc_start: 0.8500 (mptt) cc_final: 0.8110 (mmtt) REVERT: A 216 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8460 (mmtm) REVERT: A 293 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6816 (t0) REVERT: C 87 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8181 (mt-10) REVERT: C 108 GLU cc_start: 0.8402 (pt0) cc_final: 0.7790 (pm20) REVERT: C 184 MET cc_start: 0.6947 (ppp) cc_final: 0.6498 (mtp) REVERT: C 232 MET cc_start: 0.8488 (mmt) cc_final: 0.8251 (tpp) REVERT: C 309 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8291 (mp) REVERT: C 429 ASN cc_start: 0.7646 (m-40) cc_final: 0.7144 (m-40) REVERT: C 436 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6741 (m-40) REVERT: D 274 LEU cc_start: 0.8837 (mt) cc_final: 0.8589 (mt) REVERT: D 278 MET cc_start: 0.8354 (mmm) cc_final: 0.8101 (mmm) REVERT: E 50 LEU cc_start: 0.7798 (tp) cc_final: 0.7559 (tp) REVERT: E 65 GLN cc_start: 0.8121 (mt0) cc_final: 0.7796 (mt0) REVERT: E 128 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8462 (mp) REVERT: E 154 LYS cc_start: 0.8789 (mptt) cc_final: 0.8433 (mmtt) REVERT: E 265 ASP cc_start: 0.8112 (m-30) cc_final: 0.7653 (t0) REVERT: E 307 ASN cc_start: 0.8262 (m110) cc_final: 0.8018 (m-40) REVERT: F 123 MET cc_start: 0.6839 (mtp) cc_final: 0.6471 (mtt) REVERT: G 184 MET cc_start: 0.7605 (tmm) cc_final: 0.7175 (tmm) REVERT: G 211 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: G 258 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7137 (mm-30) REVERT: G 288 GLU cc_start: 0.7453 (pt0) cc_final: 0.7145 (pt0) REVERT: G 324 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7456 (mptt) REVERT: H 62 HIS cc_start: 0.8047 (m90) cc_final: 0.7792 (m-70) REVERT: H 84 LYS cc_start: 0.6131 (mmtt) cc_final: 0.5887 (mtpt) REVERT: H 111 MET cc_start: 0.8823 (mtp) cc_final: 0.8610 (mtp) REVERT: H 153 ASN cc_start: 0.7703 (p0) cc_final: 0.7018 (p0) outliers start: 34 outliers final: 28 residues processed: 282 average time/residue: 0.3700 time to fit residues: 152.6063 Evaluate side-chains 294 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 ILE 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 188 MET 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 211 GLU 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 G residue 437 ILE 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 210 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 185 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128040 restraints weight = 19347.686| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.97 r_work: 0.3195 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3048 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 8.858 24005 Z= 0.271 Chirality : 0.044 0.235 2660 Planarity : 0.004 0.044 3125 Dihedral : 7.425 119.974 2617 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.87 % Allowed : 12.69 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2228 helix: 1.64 (0.17), residues: 930 sheet: 0.21 (0.30), residues: 322 loop : -0.70 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 238 HIS 0.004 0.001 HIS A 118 PHE 0.013 0.001 PHE G 277 TYR 0.022 0.001 TYR A 225 ARG 0.009 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 804) hydrogen bonds : angle 4.17778 ( 2319) metal coordination : bond 0.00365 ( 8) metal coordination : angle 3.17866 ( 12) covalent geometry : bond 0.00337 (17775) covalent geometry : angle 0.53924 (23993) Misc. bond : bond 0.00023 ( 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: 34 poor density : 262 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.5267 (t) cc_final: 0.5047 (p) REVERT: A 95 TYR cc_start: 0.8796 (t80) cc_final: 0.8246 (t80) REVERT: A 151 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7735 (tt0) REVERT: A 154 LYS cc_start: 0.8498 (mptt) cc_final: 0.8125 (mmtt) REVERT: A 216 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8489 (mmtm) REVERT: A 261 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7454 (tt) REVERT: A 293 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6859 (t0) REVERT: C 87 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 108 GLU cc_start: 0.8404 (pt0) cc_final: 0.7814 (pm20) REVERT: C 184 MET cc_start: 0.6883 (ppp) cc_final: 0.6510 (mtp) REVERT: C 232 MET cc_start: 0.8498 (mmt) cc_final: 0.8248 (tpp) REVERT: C 309 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8306 (mp) REVERT: C 429 ASN cc_start: 0.7634 (m-40) cc_final: 0.7132 (m-40) REVERT: C 436 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6738 (m-40) REVERT: D 274 LEU cc_start: 0.8850 (mt) cc_final: 0.8598 (mt) REVERT: D 278 MET cc_start: 0.8358 (mmm) cc_final: 0.8110 (mmm) REVERT: E 50 LEU cc_start: 0.7825 (tp) cc_final: 0.7588 (tp) REVERT: E 65 GLN cc_start: 0.8130 (mt0) cc_final: 0.7818 (mt0) REVERT: E 128 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8466 (mp) REVERT: E 154 LYS cc_start: 0.8786 (mptt) cc_final: 0.8447 (mmtt) REVERT: E 265 ASP cc_start: 0.8125 (m-30) cc_final: 0.7658 (t0) REVERT: E 307 ASN cc_start: 0.8278 (m110) cc_final: 0.8031 (m-40) REVERT: F 123 MET cc_start: 0.6854 (mtp) cc_final: 0.6490 (mtt) REVERT: G 184 MET cc_start: 0.7398 (tmm) cc_final: 0.6988 (tmm) REVERT: G 211 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8601 (pt0) REVERT: G 258 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7164 (mm-30) REVERT: G 288 GLU cc_start: 0.7573 (pt0) cc_final: 0.7279 (pt0) REVERT: G 324 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7440 (mptt) REVERT: G 442 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7115 (mmtp) REVERT: G 443 LYS cc_start: 0.7337 (tttp) cc_final: 0.7127 (tttm) REVERT: H 62 HIS cc_start: 0.8072 (m90) cc_final: 0.7837 (m-70) REVERT: H 84 LYS cc_start: 0.6132 (mmtt) cc_final: 0.5888 (mtpt) REVERT: H 111 MET cc_start: 0.8828 (mtp) cc_final: 0.8614 (mtp) REVERT: H 153 ASN cc_start: 0.7699 (p0) cc_final: 0.7009 (p0) outliers start: 34 outliers final: 27 residues processed: 280 average time/residue: 0.3833 time to fit residues: 158.3328 Evaluate side-chains 293 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 309 ILE 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 188 MET 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 211 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 214 optimal weight: 0.0070 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.3604 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.173505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130318 restraints weight = 19187.478| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.00 r_work: 0.3174 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17785 Z= 0.106 Angle : 0.516 9.144 24005 Z= 0.257 Chirality : 0.043 0.234 2660 Planarity : 0.004 0.044 3125 Dihedral : 7.261 114.676 2617 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.43 % Allowed : 13.08 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2228 helix: 1.76 (0.17), residues: 931 sheet: 0.28 (0.31), residues: 322 loop : -0.63 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 367 HIS 0.003 0.001 HIS D 62 PHE 0.011 0.001 PHE C 275 TYR 0.019 0.001 TYR A 225 ARG 0.008 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 804) hydrogen bonds : angle 4.07502 ( 2319) metal coordination : bond 0.00264 ( 8) metal coordination : angle 3.14101 ( 12) covalent geometry : bond 0.00246 (17775) covalent geometry : angle 0.51164 (23993) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12173.79 seconds wall clock time: 216 minutes 52.01 seconds (13012.01 seconds total)