Starting phenix.real_space_refine on Thu Feb 15 08:47:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/02_2024/8efo_28086_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/02_2024/8efo_28086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/02_2024/8efo_28086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/02_2024/8efo_28086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/02_2024/8efo_28086_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/02_2024/8efo_28086_updated.pdb" } resolution = 2.8 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 7618 2.51 5 N 1900 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 181": "NH1" <-> "NH2" Residue "R ARG 184": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Residue "M ARG 350": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 156 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {'8QY': 1, 'CLR': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 137 Unusual residues: {'8QY': 1, 'CLR': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.41, per 1000 atoms: 0.55 Number of scatterers: 11708 At special positions: 0 Unit cell: (104, 110.24, 149.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2090 8.00 N 1900 7.00 C 7618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 17 sheets defined 45.0% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.503A pdb=" N VAL R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 132 removed outlier: 3.613A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 139 through 172 removed outlier: 3.509A pdb=" N ILE R 144 " --> pdb=" O ILE R 140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.514A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 4.166A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 227 through 242 Processing helix chain 'R' and resid 244 through 263 Processing helix chain 'R' and resid 271 through 307 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 314 through 338 removed outlier: 3.574A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 351 removed outlier: 3.528A pdb=" N CYS R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.663A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.576A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.713A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.663A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.608A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'M' and resid 68 through 97 removed outlier: 3.503A pdb=" N VAL M 96 " --> pdb=" O MET M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 132 removed outlier: 3.613A pdb=" N TYR M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Proline residue: M 124 - end of helix Processing helix chain 'M' and resid 139 through 172 removed outlier: 3.510A pdb=" N ILE M 144 " --> pdb=" O ILE M 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.513A pdb=" N LEU M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 4.166A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 227 through 242 Processing helix chain 'M' and resid 244 through 263 Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 338 removed outlier: 3.573A pdb=" N HIS M 321 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 343 through 351 removed outlier: 3.528A pdb=" N CYS M 348 " --> pdb=" O ASN M 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.832A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.861A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.565A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.768A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.701A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.628A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.703A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.629A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.535A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 92 through 99 removed outlier: 5.658A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.335A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 156 through 158 Processing sheet with id= P, first strand: chain 'E' and resid 227 through 232 removed outlier: 3.501A pdb=" N ILE E 190 " --> pdb=" O TRP E 177 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 208 through 213 601 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2738 1.33 - 1.46: 2741 1.46 - 1.58: 6358 1.58 - 1.70: 0 1.70 - 1.83: 149 Bond restraints: 11986 Sorted by residual: bond pdb=" C19 8QY M 401 " pdb=" O20 8QY M 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" C19 8QY R 401 " pdb=" O20 8QY R 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C02 8QY M 401 " pdb=" N12 8QY M 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C02 8QY R 401 " pdb=" N12 8QY R 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.94e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 91.75 - 100.20: 10 100.20 - 108.66: 734 108.66 - 117.11: 7944 117.11 - 125.57: 7433 125.57 - 134.02: 189 Bond angle restraints: 16310 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 120.63 126.54 -5.91 1.61e+00 3.86e-01 1.35e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 128.08 -4.61 1.53e+00 4.27e-01 9.08e+00 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 110.23 114.59 -4.36 1.45e+00 4.76e-01 9.03e+00 ... (remaining 16305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 7045 11.90 - 23.80: 405 23.80 - 35.71: 74 35.71 - 47.61: 34 47.61 - 59.51: 23 Dihedral angle restraints: 7581 sinusoidal: 3368 harmonic: 4213 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 57.75 35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS R 142 " pdb=" SG CYS R 142 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual 93.00 124.29 -31.29 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 7578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1695 0.086 - 0.172: 169 0.172 - 0.259: 24 0.259 - 0.345: 10 0.345 - 0.431: 10 Chirality restraints: 1908 Sorted by residual: chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1905 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " -0.008 2.00e-02 2.50e+03 1.37e-02 4.71e+00 pdb=" CG TRP E 111 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ILE B 232 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 232 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 233 " 0.011 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1746 2.77 - 3.30: 11049 3.30 - 3.84: 19733 3.84 - 4.37: 23239 4.37 - 4.90: 40066 Nonbonded interactions: 95833 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.241 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.323 2.440 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.331 2.440 nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.331 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.336 2.440 ... (remaining 95828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'R' and (resid 66 through 352 or resid 401 through 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.620 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.680 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 0.052 11986 Z= 0.284 Angle : 0.852 9.597 16310 Z= 0.452 Chirality : 0.065 0.431 1908 Planarity : 0.005 0.053 1965 Dihedral : 9.172 59.509 4848 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.93 (0.19), residues: 1423 helix: -0.48 (0.16), residues: 629 sheet: 0.09 (0.30), residues: 263 loop : -0.95 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 111 HIS 0.010 0.002 HIS E 35 PHE 0.020 0.002 PHE B 234 TYR 0.022 0.002 TYR M 254 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 231 GLU cc_start: 0.7684 (tt0) cc_final: 0.7461 (tt0) REVERT: A 272 ASP cc_start: 0.7709 (p0) cc_final: 0.7439 (p0) REVERT: A 290 TYR cc_start: 0.6417 (t80) cc_final: 0.6061 (t80) REVERT: B 44 GLN cc_start: 0.6884 (mt0) cc_final: 0.6420 (pp30) REVERT: B 188 MET cc_start: 0.7762 (mmm) cc_final: 0.7537 (mmm) outliers start: 0 outliers final: 1 residues processed: 371 average time/residue: 1.2031 time to fit residues: 482.8306 Evaluate side-chains 217 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN A 22 ASN A 188 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 91 HIS B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN M 126 GLN M 173 HIS ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11986 Z= 0.250 Angle : 0.581 8.616 16310 Z= 0.304 Chirality : 0.042 0.163 1908 Planarity : 0.004 0.042 1965 Dihedral : 8.184 56.230 2249 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.54 % Allowed : 13.33 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.74 (0.20), residues: 1423 helix: 1.54 (0.18), residues: 646 sheet: 0.24 (0.29), residues: 272 loop : -0.67 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.006 0.001 HIS B 62 PHE 0.016 0.002 PHE A 189 TYR 0.020 0.002 TYR R 108 ARG 0.004 0.001 ARG R 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6181 (ttm-80) REVERT: R 140 ILE cc_start: 0.7863 (tp) cc_final: 0.7639 (tt) REVERT: R 231 GLU cc_start: 0.7720 (tt0) cc_final: 0.7441 (tt0) REVERT: A 8 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 33 ILE cc_start: 0.7076 (mt) cc_final: 0.6739 (mt) REVERT: B 217 MET cc_start: 0.6709 (pmm) cc_final: 0.6506 (pmm) REVERT: B 331 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8220 (t) REVERT: E 87 ARG cc_start: 0.7237 (mmm160) cc_final: 0.7031 (mmm160) REVERT: M 67 MET cc_start: 0.4738 (tmt) cc_final: 0.4162 (ttm) REVERT: M 86 PHE cc_start: 0.7340 (t80) cc_final: 0.6862 (t80) REVERT: M 144 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7130 (mp) REVERT: M 218 ASP cc_start: 0.6202 (m-30) cc_final: 0.5753 (m-30) REVERT: M 275 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.7187 (tmm160) REVERT: M 278 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6010 (tpp80) REVERT: F 340 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7337 (t) outliers start: 32 outliers final: 9 residues processed: 247 average time/residue: 1.2664 time to fit residues: 338.4520 Evaluate side-chains 201 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN M 185 ASN M 225 HIS M 330 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11986 Z= 0.225 Angle : 0.532 9.119 16310 Z= 0.277 Chirality : 0.041 0.154 1908 Planarity : 0.004 0.036 1965 Dihedral : 7.697 56.836 2249 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.49 % Allowed : 15.71 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.14 (0.21), residues: 1423 helix: 1.96 (0.19), residues: 652 sheet: 0.13 (0.30), residues: 277 loop : -0.44 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.002 TYR M 254 ARG 0.009 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6236 (ttm-80) REVERT: R 231 GLU cc_start: 0.7771 (tt0) cc_final: 0.7468 (tt0) REVERT: R 282 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6991 (ttt-90) REVERT: A 53 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7483 (mmt) REVERT: A 276 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 33 ILE cc_start: 0.7163 (mt) cc_final: 0.6879 (mt) REVERT: B 325 MET cc_start: 0.7307 (tpp) cc_final: 0.6849 (tpt) REVERT: B 331 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 28 ILE cc_start: 0.7461 (pt) cc_final: 0.7245 (pp) REVERT: E 11 LEU cc_start: 0.7425 (mm) cc_final: 0.6894 (tp) REVERT: M 67 MET cc_start: 0.4981 (tmt) cc_final: 0.4392 (ttm) REVERT: M 74 MET cc_start: 0.7827 (mmm) cc_final: 0.7626 (mmp) REVERT: M 86 PHE cc_start: 0.7411 (t80) cc_final: 0.6968 (t80) REVERT: M 144 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7133 (mp) REVERT: F 340 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7303 (t) outliers start: 44 outliers final: 13 residues processed: 225 average time/residue: 1.2630 time to fit residues: 306.5549 Evaluate side-chains 190 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 255 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11986 Z= 0.198 Angle : 0.500 8.394 16310 Z= 0.261 Chirality : 0.040 0.151 1908 Planarity : 0.004 0.034 1965 Dihedral : 7.263 56.190 2249 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.49 % Allowed : 16.90 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.34 (0.21), residues: 1423 helix: 2.16 (0.19), residues: 654 sheet: 0.09 (0.30), residues: 278 loop : -0.33 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE A 189 TYR 0.012 0.001 TYR E 191 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7513 (tpp) cc_final: 0.7205 (tpp) REVERT: R 89 PHE cc_start: 0.7463 (m-10) cc_final: 0.7069 (m-10) REVERT: R 97 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6355 (ttm-80) REVERT: R 231 GLU cc_start: 0.7750 (tt0) cc_final: 0.7450 (tt0) REVERT: A 245 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: A 276 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 325 MET cc_start: 0.7272 (tpp) cc_final: 0.6949 (tpt) REVERT: C 47 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6762 (mt-10) REVERT: E 3 GLN cc_start: 0.7425 (mt0) cc_final: 0.6965 (mt0) REVERT: E 11 LEU cc_start: 0.7492 (mm) cc_final: 0.6956 (tp) REVERT: M 67 MET cc_start: 0.5080 (tmt) cc_final: 0.4612 (ttm) REVERT: M 74 MET cc_start: 0.7873 (mmm) cc_final: 0.7658 (mmp) REVERT: M 278 ARG cc_start: 0.7262 (tpt170) cc_final: 0.6375 (tpp80) REVERT: F 340 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7286 (t) outliers start: 44 outliers final: 17 residues processed: 218 average time/residue: 1.2790 time to fit residues: 301.0469 Evaluate side-chains 192 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11986 Z= 0.244 Angle : 0.532 10.592 16310 Z= 0.275 Chirality : 0.041 0.149 1908 Planarity : 0.004 0.039 1965 Dihedral : 7.344 57.212 2249 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.81 % Allowed : 17.70 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.40 (0.22), residues: 1423 helix: 2.23 (0.19), residues: 656 sheet: 0.05 (0.30), residues: 275 loop : -0.28 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.002 TYR R 130 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7572 (tpp) cc_final: 0.7277 (tpp) REVERT: R 89 PHE cc_start: 0.7416 (m-10) cc_final: 0.7061 (m-10) REVERT: R 97 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6469 (ttm-80) REVERT: R 231 GLU cc_start: 0.7767 (tt0) cc_final: 0.7463 (tt0) REVERT: R 282 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6982 (ttt-90) REVERT: A 245 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: A 276 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 44 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6550 (mp10) REVERT: B 154 ASP cc_start: 0.8007 (m-30) cc_final: 0.7706 (m-30) REVERT: B 325 MET cc_start: 0.7233 (tpp) cc_final: 0.6969 (tpt) REVERT: C 28 ILE cc_start: 0.7656 (pt) cc_final: 0.7326 (pp) REVERT: E 3 GLN cc_start: 0.7426 (mt0) cc_final: 0.6974 (mt0) REVERT: E 5 VAL cc_start: 0.8002 (m) cc_final: 0.7716 (p) REVERT: M 144 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7157 (mp) REVERT: F 340 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7316 (t) REVERT: F 341 ASP cc_start: 0.7672 (t0) cc_final: 0.7150 (m-30) outliers start: 48 outliers final: 26 residues processed: 218 average time/residue: 1.2458 time to fit residues: 293.5636 Evaluate side-chains 210 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 205 MET Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN M 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11986 Z= 0.289 Angle : 0.565 10.140 16310 Z= 0.290 Chirality : 0.041 0.153 1908 Planarity : 0.004 0.040 1965 Dihedral : 7.470 57.949 2249 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.37 % Allowed : 17.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.29 (0.22), residues: 1423 helix: 2.12 (0.19), residues: 656 sheet: -0.03 (0.31), residues: 266 loop : -0.28 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.007 0.001 HIS B 62 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.002 TYR E 191 ARG 0.015 0.001 ARG M 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 186 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7726 (tpp) cc_final: 0.7450 (tpp) REVERT: R 89 PHE cc_start: 0.7409 (m-10) cc_final: 0.7100 (m-10) REVERT: R 97 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6505 (ttm-80) REVERT: R 231 GLU cc_start: 0.7799 (tt0) cc_final: 0.7492 (tt0) REVERT: R 282 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6967 (ttt-90) REVERT: A 21 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7483 (ttm110) REVERT: A 245 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: B 44 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: B 304 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7582 (mtp-110) REVERT: B 325 MET cc_start: 0.7177 (tpp) cc_final: 0.6912 (tpt) REVERT: C 28 ILE cc_start: 0.7740 (pt) cc_final: 0.7377 (pp) REVERT: E 3 GLN cc_start: 0.7414 (mt0) cc_final: 0.7009 (mt0) REVERT: M 144 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7220 (mp) REVERT: F 340 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7306 (t) REVERT: F 341 ASP cc_start: 0.7563 (t0) cc_final: 0.7227 (m-30) outliers start: 55 outliers final: 29 residues processed: 222 average time/residue: 1.3049 time to fit residues: 312.7869 Evaluate side-chains 212 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 205 MET Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11986 Z= 0.197 Angle : 0.520 9.865 16310 Z= 0.267 Chirality : 0.040 0.151 1908 Planarity : 0.004 0.034 1965 Dihedral : 7.112 58.192 2247 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.65 % Allowed : 19.13 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.38 (0.22), residues: 1423 helix: 2.24 (0.19), residues: 656 sheet: -0.07 (0.31), residues: 261 loop : -0.27 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR E 191 ARG 0.004 0.000 ARG R 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7686 (tpp) cc_final: 0.7415 (tpp) REVERT: R 89 PHE cc_start: 0.7367 (m-10) cc_final: 0.7127 (m-10) REVERT: R 97 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6521 (ttm-80) REVERT: R 231 GLU cc_start: 0.7756 (tt0) cc_final: 0.7463 (tt0) REVERT: A 21 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7483 (ttm110) REVERT: A 276 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 313 ARG cc_start: 0.7432 (ptp-110) cc_final: 0.7160 (ptp-110) REVERT: B 44 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6445 (mp10) REVERT: B 101 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8037 (ptm) REVERT: B 304 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7520 (mtp-110) REVERT: B 325 MET cc_start: 0.7281 (tpp) cc_final: 0.7026 (tpt) REVERT: C 28 ILE cc_start: 0.7787 (pt) cc_final: 0.7396 (pp) REVERT: C 32 LYS cc_start: 0.7576 (tptt) cc_final: 0.7205 (tptt) REVERT: C 47 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6872 (mt-10) REVERT: E 3 GLN cc_start: 0.7476 (mt0) cc_final: 0.7035 (mt0) REVERT: E 5 VAL cc_start: 0.8196 (m) cc_final: 0.7863 (p) REVERT: M 144 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7248 (mp) REVERT: M 218 ASP cc_start: 0.7098 (t0) cc_final: 0.6800 (p0) REVERT: F 340 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7248 (t) outliers start: 46 outliers final: 28 residues processed: 218 average time/residue: 1.3870 time to fit residues: 324.5938 Evaluate side-chains 208 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11986 Z= 0.191 Angle : 0.531 10.457 16310 Z= 0.270 Chirality : 0.040 0.147 1908 Planarity : 0.004 0.054 1965 Dihedral : 6.924 59.900 2247 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.49 % Allowed : 19.84 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.38 (0.22), residues: 1423 helix: 2.29 (0.19), residues: 656 sheet: -0.19 (0.30), residues: 268 loop : -0.26 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR E 191 ARG 0.014 0.001 ARG M 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7659 (tpp) cc_final: 0.7370 (tpp) REVERT: R 89 PHE cc_start: 0.7346 (m-10) cc_final: 0.7116 (m-10) REVERT: R 97 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6510 (ttm-80) REVERT: R 231 GLU cc_start: 0.7753 (tt0) cc_final: 0.7450 (tt0) REVERT: A 53 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6602 (mpt) REVERT: B 44 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6485 (mp10) REVERT: B 101 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8037 (ptm) REVERT: B 325 MET cc_start: 0.7301 (tpp) cc_final: 0.7070 (tpt) REVERT: B 331 SER cc_start: 0.8686 (t) cc_final: 0.8444 (t) REVERT: C 28 ILE cc_start: 0.7796 (pt) cc_final: 0.7454 (pp) REVERT: C 47 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6717 (mt-10) REVERT: E 3 GLN cc_start: 0.7418 (mt0) cc_final: 0.7096 (mt0) REVERT: M 144 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7275 (mp) REVERT: F 340 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7250 (t) outliers start: 44 outliers final: 29 residues processed: 223 average time/residue: 1.3407 time to fit residues: 321.9375 Evaluate side-chains 216 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11986 Z= 0.201 Angle : 0.529 10.100 16310 Z= 0.271 Chirality : 0.040 0.149 1908 Planarity : 0.004 0.049 1965 Dihedral : 6.847 55.209 2247 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.89 % Allowed : 20.16 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.37 (0.22), residues: 1423 helix: 2.29 (0.19), residues: 656 sheet: -0.18 (0.30), residues: 276 loop : -0.26 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR E 191 ARG 0.013 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7659 (tpp) cc_final: 0.7385 (tpp) REVERT: R 89 PHE cc_start: 0.7369 (m-10) cc_final: 0.7159 (m-10) REVERT: R 97 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6483 (ttm-80) REVERT: R 231 GLU cc_start: 0.7755 (tt0) cc_final: 0.7450 (tt0) REVERT: A 53 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6824 (mpt) REVERT: B 44 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: B 228 ASP cc_start: 0.7234 (p0) cc_final: 0.6950 (p0) REVERT: B 325 MET cc_start: 0.7269 (tpp) cc_final: 0.7044 (tpt) REVERT: C 28 ILE cc_start: 0.7806 (pt) cc_final: 0.7467 (pp) REVERT: C 47 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6800 (mt-10) REVERT: E 3 GLN cc_start: 0.7412 (mt0) cc_final: 0.7078 (mt0) REVERT: M 144 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7285 (mp) REVERT: F 340 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7241 (t) outliers start: 49 outliers final: 30 residues processed: 221 average time/residue: 1.3385 time to fit residues: 318.7607 Evaluate side-chains 212 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.0010 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11986 Z= 0.217 Angle : 0.552 10.069 16310 Z= 0.281 Chirality : 0.040 0.148 1908 Planarity : 0.004 0.068 1965 Dihedral : 6.708 55.127 2247 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.10 % Allowed : 21.35 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.31 (0.22), residues: 1423 helix: 2.25 (0.19), residues: 656 sheet: -0.19 (0.31), residues: 266 loop : -0.34 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR A 230 ARG 0.013 0.001 ARG M 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7663 (tpp) cc_final: 0.7388 (tpp) REVERT: R 97 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6460 (ttm-80) REVERT: R 231 GLU cc_start: 0.7763 (tt0) cc_final: 0.7457 (tt0) REVERT: B 325 MET cc_start: 0.7295 (tpp) cc_final: 0.7072 (tpt) REVERT: C 28 ILE cc_start: 0.7816 (pt) cc_final: 0.7471 (pp) REVERT: C 47 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6811 (mt-10) REVERT: E 3 GLN cc_start: 0.7350 (mt0) cc_final: 0.7036 (mt0) REVERT: M 144 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7279 (mp) REVERT: F 340 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.7246 (t) outliers start: 39 outliers final: 31 residues processed: 211 average time/residue: 1.3314 time to fit residues: 303.1197 Evaluate side-chains 205 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 282 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117083 restraints weight = 15689.484| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.80 r_work: 0.3309 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11986 Z= 0.216 Angle : 0.556 9.774 16310 Z= 0.281 Chirality : 0.040 0.148 1908 Planarity : 0.004 0.042 1965 Dihedral : 6.698 55.134 2247 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.33 % Allowed : 21.43 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.28 (0.22), residues: 1423 helix: 2.24 (0.19), residues: 656 sheet: -0.29 (0.30), residues: 273 loop : -0.32 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR A 230 ARG 0.012 0.001 ARG B 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5422.27 seconds wall clock time: 96 minutes 56.75 seconds (5816.75 seconds total)