Starting phenix.real_space_refine on Thu Feb 15 09:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/02_2024/8efl_28085_updated.pdb" } 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= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 Cl 6 4.86 5 C 7645 2.51 5 N 1908 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 282": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 265": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11750 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: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} 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: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'TRANS': 22} Chain: "R" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.69, per 1000 atoms: 0.57 Number of scatterers: 11750 At special positions: 0 Unit cell: (106.029, 116.739, 153.153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 98 16.00 O 2093 8.00 N 1908 7.00 C 7645 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=2.04 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: 4.88 Conformation dependent library (CDL) restraints added in 2.4 seconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 15 sheets defined 45.4% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'R' and resid 67 through 97 Processing helix chain 'R' and resid 104 through 121 Processing helix chain 'R' and resid 123 through 132 Processing helix chain 'R' and resid 139 through 172 Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.826A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 4.031A 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 263 removed outlier: 5.333A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix 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: 3.939A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.283A 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 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 216 removed outlier: 4.652A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (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 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 11 through 23 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 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'M' and resid 67 through 97 Processing helix chain 'M' and resid 104 through 132 removed outlier: 3.995A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 4.446A 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: 3.689A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.807A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.745A 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 263 removed outlier: 5.201A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 339 removed outlier: 3.745A 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 Processing helix chain 'F' and resid 333 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 323 removed outlier: 6.749A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.772A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.661A 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: 6.734A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.791A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.765A 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: 7.159A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.213A 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: 6.809A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.503A 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: 6.852A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.003A 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: 6.859A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.949A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 156 through 160 Processing sheet with id= N, first strand: chain 'E' and resid 226 through 232 removed outlier: 5.889A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG E 181 " --> pdb=" O PRO E 186 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 208 through 213 633 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1808 1.30 - 1.43: 3148 1.43 - 1.56: 6917 1.56 - 1.69: 9 1.69 - 1.82: 151 Bond restraints: 12033 Sorted by residual: bond pdb=" C03 WH9 R 401 " pdb=" N01 WH9 R 401 " ideal model delta sigma weight residual 1.477 1.316 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C03 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.477 1.316 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" C05 WH9 R 401 " pdb=" N02 WH9 R 401 " ideal model delta sigma weight residual 1.477 1.348 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C05 WH9 M 401 " pdb=" N02 WH9 M 401 " ideal model delta sigma weight residual 1.477 1.348 0.129 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C07 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.431 1.322 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 12028 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.95: 250 105.95 - 112.98: 6676 112.98 - 120.02: 4018 120.02 - 127.05: 5298 127.05 - 134.08: 137 Bond angle restraints: 16379 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 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C06 WH9 R 401 " pdb=" C04 WH9 R 401 " pdb="CL2 WH9 R 401 " ideal model delta sigma weight residual 131.83 120.28 11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C06 WH9 M 401 " pdb=" C04 WH9 M 401 " pdb="CL2 WH9 M 401 " ideal model delta sigma weight residual 131.83 120.29 11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C02 WH9 M 401 " pdb=" C04 WH9 M 401 " pdb="CL2 WH9 M 401 " ideal model delta sigma weight residual 108.07 119.31 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C02 WH9 R 401 " pdb=" C04 WH9 R 401 " pdb="CL2 WH9 R 401 " ideal model delta sigma weight residual 108.07 119.22 -11.15 3.00e+00 1.11e-01 1.38e+01 ... (remaining 16374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 7219 14.15 - 28.29: 293 28.29 - 42.44: 62 42.44 - 56.58: 15 56.58 - 70.73: 2 Dihedral angle restraints: 7591 sinusoidal: 3363 harmonic: 4228 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE B 81 " pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 7588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1697 0.088 - 0.176: 170 0.176 - 0.264: 25 0.264 - 0.352: 8 0.352 - 0.440: 11 Chirality restraints: 1911 Sorted by residual: chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.83e+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 -2.74 0.42 2.00e-01 2.50e+01 4.46e+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 -2.73 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1908 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 236 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 278 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ARG R 278 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG R 278 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 279 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.025 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2218 2.79 - 3.32: 10679 3.32 - 3.84: 19103 3.84 - 4.37: 21544 4.37 - 4.90: 38737 Nonbonded interactions: 92281 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.259 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.279 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.304 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.321 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.330 2.440 ... (remaining 92276 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' } 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: 0.490 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: 2.950 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.610 Find NCS groups from input model: 0.430 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.006 0.161 12033 Z= 0.347 Angle : 0.894 11.546 16379 Z= 0.468 Chirality : 0.066 0.440 1911 Planarity : 0.006 0.075 1969 Dihedral : 8.667 70.730 4848 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.35 (0.20), residues: 1428 helix: 1.12 (0.17), residues: 664 sheet: 0.57 (0.30), residues: 283 loop : -1.19 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.005 0.001 HIS B 54 PHE 0.026 0.002 PHE A 189 TYR 0.024 0.002 TYR R 108 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.291 Fit side-chains REVERT: R 260 ARG cc_start: 0.7467 (tpt90) cc_final: 0.7009 (tpp80) REVERT: A 44 SER cc_start: 0.7619 (m) cc_final: 0.7127 (p) REVERT: A 309 ASP cc_start: 0.7249 (m-30) cc_final: 0.7039 (m-30) REVERT: B 150 ARG cc_start: 0.8430 (mmt-90) cc_final: 0.8179 (mpt180) REVERT: B 175 GLN cc_start: 0.7608 (mm110) cc_final: 0.7160 (mm110) REVERT: B 189 SER cc_start: 0.8838 (p) cc_final: 0.8480 (t) REVERT: E 167 LEU cc_start: 0.7827 (tp) cc_final: 0.7541 (tp) REVERT: M 266 MET cc_start: 0.5980 (tmt) cc_final: 0.5721 (ttp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2488 time to fit residues: 84.7101 Evaluate side-chains 160 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.0040 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 190 ASN B 35 ASN B 88 ASN B 91 HIS B 155 ASN B 266 HIS B 293 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN M 106 ASN M 330 ASN M 334 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12033 Z= 0.139 Angle : 0.464 6.615 16379 Z= 0.241 Chirality : 0.038 0.147 1911 Planarity : 0.004 0.058 1969 Dihedral : 6.259 68.614 2236 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.90 % Allowed : 7.04 % Favored : 91.06 % 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: 1.60 (0.21), residues: 1428 helix: 2.57 (0.18), residues: 668 sheet: 0.53 (0.30), residues: 282 loop : -0.83 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.021 0.001 PHE A 189 TYR 0.013 0.001 TYR R 151 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.267 Fit side-chains REVERT: R 310 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5867 (tp) REVERT: A 276 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 309 ASP cc_start: 0.7288 (m-30) cc_final: 0.7002 (m-30) REVERT: A 350 ASP cc_start: 0.7394 (t0) cc_final: 0.7145 (m-30) REVERT: B 175 GLN cc_start: 0.7629 (mm110) cc_final: 0.7399 (mm-40) REVERT: B 325 MET cc_start: 0.7469 (tpp) cc_final: 0.7100 (mmt) outliers start: 24 outliers final: 16 residues processed: 179 average time/residue: 0.2125 time to fit residues: 56.3725 Evaluate side-chains 161 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN R 190 ASN R 232 ASN A 213 HIS B 75 GLN E 180 GLN M 111 ASN M 190 ASN M 334 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 12033 Z= 0.665 Angle : 0.806 10.484 16379 Z= 0.410 Chirality : 0.051 0.230 1911 Planarity : 0.006 0.050 1969 Dihedral : 8.183 71.005 2236 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.56 % Allowed : 8.39 % Favored : 88.05 % 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: 0.87 (0.21), residues: 1428 helix: 1.82 (0.19), residues: 656 sheet: 0.31 (0.29), residues: 293 loop : -0.98 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 99 HIS 0.013 0.002 HIS B 54 PHE 0.036 0.003 PHE R 154 TYR 0.032 0.003 TYR R 301 ARG 0.008 0.001 ARG R 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 1.298 Fit side-chains REVERT: R 310 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6918 (tp) REVERT: A 44 SER cc_start: 0.8015 (m) cc_final: 0.7459 (p) REVERT: A 240 MET cc_start: 0.3867 (OUTLIER) cc_final: 0.3568 (mtt) REVERT: B 175 GLN cc_start: 0.7766 (mm110) cc_final: 0.7416 (mm110) REVERT: E 141 MET cc_start: 0.8663 (mmm) cc_final: 0.7760 (mmm) REVERT: E 232 GLN cc_start: 0.7869 (pp30) cc_final: 0.7591 (pp30) REVERT: M 283 MET cc_start: 0.7847 (tpp) cc_final: 0.7479 (tpp) outliers start: 45 outliers final: 29 residues processed: 199 average time/residue: 0.2399 time to fit residues: 68.0251 Evaluate side-chains 166 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12033 Z= 0.156 Angle : 0.486 6.919 16379 Z= 0.253 Chirality : 0.039 0.151 1911 Planarity : 0.004 0.045 1969 Dihedral : 6.747 66.678 2236 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.22 % Allowed : 11.63 % Favored : 86.16 % 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: 1.51 (0.21), residues: 1428 helix: 2.55 (0.19), residues: 663 sheet: 0.37 (0.29), residues: 287 loop : -0.86 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.002 0.000 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.012 0.001 TYR M 151 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.282 Fit side-chains REVERT: R 310 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7058 (tp) REVERT: A 32 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7444 (mtm110) REVERT: B 175 GLN cc_start: 0.7694 (mm110) cc_final: 0.7405 (mm110) REVERT: B 176 GLN cc_start: 0.8507 (pt0) cc_final: 0.8281 (pt0) REVERT: B 197 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7715 (mtm180) REVERT: B 269 ILE cc_start: 0.7810 (mt) cc_final: 0.7583 (tp) REVERT: E 193 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7789 (ptm) REVERT: M 283 MET cc_start: 0.7639 (tpp) cc_final: 0.7266 (tpp) outliers start: 28 outliers final: 19 residues processed: 154 average time/residue: 0.2244 time to fit residues: 51.2857 Evaluate side-chains 143 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 50.0000 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12033 Z= 0.164 Angle : 0.468 5.933 16379 Z= 0.242 Chirality : 0.038 0.149 1911 Planarity : 0.003 0.036 1969 Dihedral : 6.464 66.773 2236 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 11.95 % Favored : 85.52 % 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: 1.74 (0.22), residues: 1428 helix: 2.81 (0.19), residues: 665 sheet: 0.31 (0.28), residues: 289 loop : -0.74 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.013 0.001 TYR R 151 ARG 0.004 0.000 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.439 Fit side-chains REVERT: R 310 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7094 (tp) REVERT: B 175 GLN cc_start: 0.7671 (mm110) cc_final: 0.7444 (mm110) REVERT: E 141 MET cc_start: 0.8515 (mmm) cc_final: 0.7449 (mmm) REVERT: M 283 MET cc_start: 0.7627 (tpp) cc_final: 0.7303 (tpp) REVERT: M 333 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7759 (mp) REVERT: F 354 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7092 (m-80) outliers start: 32 outliers final: 21 residues processed: 150 average time/residue: 0.2289 time to fit residues: 50.4685 Evaluate side-chains 148 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN M 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12033 Z= 0.231 Angle : 0.503 6.464 16379 Z= 0.258 Chirality : 0.039 0.150 1911 Planarity : 0.003 0.039 1969 Dihedral : 6.601 66.237 2236 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.77 % Allowed : 12.58 % Favored : 84.65 % 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: 1.76 (0.22), residues: 1428 helix: 2.81 (0.19), residues: 662 sheet: 0.16 (0.28), residues: 292 loop : -0.56 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.015 0.001 PHE A 189 TYR 0.015 0.001 TYR E 94 ARG 0.003 0.000 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.346 Fit side-chains REVERT: R 266 MET cc_start: 0.6487 (tpp) cc_final: 0.6272 (tpp) REVERT: R 310 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7227 (tp) REVERT: A 44 SER cc_start: 0.8196 (m) cc_final: 0.7718 (p) REVERT: B 175 GLN cc_start: 0.7699 (mm110) cc_final: 0.7392 (mm110) REVERT: E 141 MET cc_start: 0.8557 (mmm) cc_final: 0.7515 (mmm) REVERT: E 193 MET cc_start: 0.8122 (ptm) cc_final: 0.7736 (ptt) REVERT: M 283 MET cc_start: 0.7660 (tpp) cc_final: 0.7342 (tpp) REVERT: F 354 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7302 (m-80) outliers start: 35 outliers final: 29 residues processed: 153 average time/residue: 0.2237 time to fit residues: 50.5210 Evaluate side-chains 154 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12033 Z= 0.270 Angle : 0.526 7.739 16379 Z= 0.269 Chirality : 0.040 0.155 1911 Planarity : 0.004 0.040 1969 Dihedral : 6.690 63.932 2236 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 13.05 % Favored : 83.78 % 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: 1.66 (0.22), residues: 1428 helix: 2.76 (0.19), residues: 657 sheet: 0.08 (0.28), residues: 292 loop : -0.60 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.017 0.001 TYR E 94 ARG 0.003 0.000 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.365 Fit side-chains REVERT: R 266 MET cc_start: 0.6516 (tpp) cc_final: 0.6060 (tpt) REVERT: R 310 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7368 (tp) REVERT: M 283 MET cc_start: 0.7733 (tpp) cc_final: 0.7395 (tpp) REVERT: F 354 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7457 (m-80) outliers start: 40 outliers final: 34 residues processed: 155 average time/residue: 0.2323 time to fit residues: 53.7485 Evaluate side-chains 158 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN E 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12033 Z= 0.263 Angle : 0.523 7.318 16379 Z= 0.268 Chirality : 0.040 0.153 1911 Planarity : 0.004 0.042 1969 Dihedral : 6.624 62.456 2236 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.40 % Allowed : 13.37 % Favored : 83.23 % 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: 1.65 (0.22), residues: 1428 helix: 2.72 (0.19), residues: 659 sheet: 0.14 (0.29), residues: 287 loop : -0.62 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE E 240 TYR 0.015 0.001 TYR E 94 ARG 0.004 0.000 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 1.337 Fit side-chains REVERT: R 266 MET cc_start: 0.6592 (tpp) cc_final: 0.6197 (tpt) REVERT: R 310 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7468 (tp) REVERT: E 193 MET cc_start: 0.8183 (ptm) cc_final: 0.7969 (ptt) REVERT: M 283 MET cc_start: 0.7744 (tpp) cc_final: 0.7416 (tpp) REVERT: F 354 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7423 (m-80) outliers start: 43 outliers final: 39 residues processed: 159 average time/residue: 0.2279 time to fit residues: 53.2181 Evaluate side-chains 165 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 0.0570 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12033 Z= 0.141 Angle : 0.462 7.513 16379 Z= 0.238 Chirality : 0.038 0.141 1911 Planarity : 0.003 0.038 1969 Dihedral : 6.187 57.984 2236 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.53 % Allowed : 14.08 % Favored : 83.39 % 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: 1.86 (0.22), residues: 1428 helix: 2.90 (0.19), residues: 663 sheet: 0.33 (0.30), residues: 280 loop : -0.60 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR M 151 ARG 0.004 0.000 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.371 Fit side-chains REVERT: R 266 MET cc_start: 0.6417 (tpp) cc_final: 0.6158 (tpp) REVERT: R 310 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7414 (tp) REVERT: A 209 LYS cc_start: 0.8556 (pttt) cc_final: 0.8307 (ptmt) REVERT: E 141 MET cc_start: 0.8422 (mmm) cc_final: 0.7403 (mmm) REVERT: M 283 MET cc_start: 0.7660 (tpp) cc_final: 0.7340 (tpp) REVERT: F 354 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7298 (m-80) outliers start: 32 outliers final: 28 residues processed: 152 average time/residue: 0.2341 time to fit residues: 51.9614 Evaluate side-chains 157 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12033 Z= 0.306 Angle : 0.550 7.520 16379 Z= 0.281 Chirality : 0.041 0.169 1911 Planarity : 0.004 0.040 1969 Dihedral : 6.658 59.972 2236 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.69 % Allowed : 14.00 % Favored : 83.31 % 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: 1.65 (0.22), residues: 1428 helix: 2.75 (0.19), residues: 655 sheet: -0.03 (0.28), residues: 308 loop : -0.52 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS E 233 PHE 0.015 0.002 PHE A 189 TYR 0.020 0.002 TYR B 289 ARG 0.003 0.000 ARG M 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.462 Fit side-chains REVERT: R 266 MET cc_start: 0.6663 (tpp) cc_final: 0.6279 (tpt) REVERT: R 310 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7513 (tp) REVERT: E 141 MET cc_start: 0.8504 (mmm) cc_final: 0.7473 (mmm) REVERT: E 193 MET cc_start: 0.8386 (ptm) cc_final: 0.8164 (ptt) REVERT: M 283 MET cc_start: 0.7756 (tpp) cc_final: 0.7428 (tpp) REVERT: F 354 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7502 (m-80) outliers start: 34 outliers final: 32 residues processed: 154 average time/residue: 0.2460 time to fit residues: 55.4961 Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 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 176 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.173017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131334 restraints weight = 12326.022| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.14 r_work: 0.3061 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12033 Z= 0.149 Angle : 0.462 7.325 16379 Z= 0.239 Chirality : 0.038 0.145 1911 Planarity : 0.003 0.038 1969 Dihedral : 6.177 55.787 2236 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.53 % Allowed : 14.00 % Favored : 83.47 % 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: 1.86 (0.22), residues: 1428 helix: 2.90 (0.19), residues: 663 sheet: 0.24 (0.30), residues: 283 loop : -0.54 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR M 151 ARG 0.004 0.000 ARG M 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.09 seconds wall clock time: 48 minutes 56.69 seconds (2936.69 seconds total)