Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 07:06:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_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_28085/04_2023/8efl_28085_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/04_2023/8efl_28085_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 6.57, per 1000 atoms: 0.56 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: 4.74 Conformation dependent library (CDL) restraints added in 1.9 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: 0.97 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: 3.34 Time building geometry restraints manager: 5.12 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: 6711 14.15 - 28.29: 261 28.29 - 42.44: 43 42.44 - 56.58: 8 56.58 - 70.73: 2 Dihedral angle restraints: 7025 sinusoidal: 2797 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 7022 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: 0.600 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: 3.580 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.350 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- 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 : 8.273 70.730 4282 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 % 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 *********************** 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 : 1.257 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2491 time to fit residues: 84.8485 Evaluate side-chains 156 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9496 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 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 111 ASN R 173 HIS R 190 ASN B 35 ASN B 62 HIS 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12033 Z= 0.157 Angle : 0.475 6.313 16379 Z= 0.247 Chirality : 0.038 0.148 1911 Planarity : 0.004 0.060 1969 Dihedral : 5.096 69.471 1670 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 2.14 % 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: 1.61 (0.21), residues: 1428 helix: 2.60 (0.18), residues: 668 sheet: 0.58 (0.30), residues: 274 loop : -0.87 (0.25), residues: 486 *********************** 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 196 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.314 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 186 average time/residue: 0.2176 time to fit residues: 60.0494 Evaluate side-chains 156 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1064 time to fit residues: 5.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 0.0060 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN E 180 GLN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 12033 Z= 0.279 Angle : 0.565 8.666 16379 Z= 0.290 Chirality : 0.041 0.156 1911 Planarity : 0.004 0.050 1969 Dihedral : 5.728 69.912 1670 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 1.90 % 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: 1.63 (0.21), residues: 1428 helix: 2.64 (0.19), residues: 662 sheet: 0.42 (0.29), residues: 286 loop : -0.76 (0.25), residues: 480 *********************** 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 171 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.393 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 160 average time/residue: 0.2377 time to fit residues: 55.3015 Evaluate side-chains 144 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1030 time to fit residues: 4.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 9.9990 chunk 96 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3233 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= 0.158 Angle : 0.460 5.263 16379 Z= 0.238 Chirality : 0.038 0.147 1911 Planarity : 0.003 0.042 1969 Dihedral : 5.346 68.891 1670 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 0.79 % 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: 1.91 (0.21), residues: 1428 helix: 2.91 (0.19), residues: 664 sheet: 0.57 (0.29), residues: 279 loop : -0.70 (0.26), residues: 485 *********************** 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 153 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.425 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 148 average time/residue: 0.2395 time to fit residues: 52.0414 Evaluate side-chains 141 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1088 time to fit residues: 3.1718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12033 Z= 0.262 Angle : 0.523 7.983 16379 Z= 0.267 Chirality : 0.040 0.144 1911 Planarity : 0.004 0.041 1969 Dihedral : 5.621 68.420 1670 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.90 % 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: 1.82 (0.22), residues: 1428 helix: 2.84 (0.19), residues: 659 sheet: 0.29 (0.29), residues: 295 loop : -0.56 (0.26), residues: 474 *********************** 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 164 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.345 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 156 average time/residue: 0.2435 time to fit residues: 55.2938 Evaluate side-chains 143 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1411 time to fit residues: 5.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12033 Z= 0.238 Angle : 0.507 6.773 16379 Z= 0.259 Chirality : 0.039 0.148 1911 Planarity : 0.003 0.041 1969 Dihedral : 5.602 66.558 1670 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 1.34 % 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: 1.80 (0.22), residues: 1428 helix: 2.82 (0.19), residues: 659 sheet: 0.35 (0.29), residues: 287 loop : -0.60 (0.26), residues: 482 *********************** 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 151 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.423 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 144 average time/residue: 0.2496 time to fit residues: 51.8135 Evaluate side-chains 140 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1533 time to fit residues: 4.4970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 12033 Z= 0.381 Angle : 0.605 8.395 16379 Z= 0.305 Chirality : 0.042 0.155 1911 Planarity : 0.004 0.047 1969 Dihedral : 6.131 64.780 1670 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.71 % 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: 1.55 (0.22), residues: 1428 helix: 2.58 (0.19), residues: 653 sheet: 0.34 (0.30), residues: 289 loop : -0.72 (0.26), residues: 486 *********************** 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 140 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.450 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 136 average time/residue: 0.2452 time to fit residues: 48.7034 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1082 time to fit residues: 3.2924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 0.0060 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 0.0270 chunk 118 optimal weight: 0.8980 overall best weight: 0.5254 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.4104 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= 0.129 Angle : 0.457 6.956 16379 Z= 0.236 Chirality : 0.038 0.142 1911 Planarity : 0.003 0.037 1969 Dihedral : 5.541 58.108 1670 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 0.63 % 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: 1.84 (0.22), residues: 1428 helix: 2.88 (0.19), residues: 659 sheet: 0.36 (0.30), residues: 282 loop : -0.62 (0.27), residues: 487 *********************** 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 142 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.512 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 139 average time/residue: 0.2575 time to fit residues: 52.2751 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1116 time to fit residues: 2.3979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 83 optimal weight: 0.0670 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4102 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= 0.137 Angle : 0.464 6.558 16379 Z= 0.238 Chirality : 0.038 0.152 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.370 59.623 1670 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 0.24 % 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: 2.01 (0.22), residues: 1428 helix: 3.03 (0.19), residues: 659 sheet: 0.44 (0.30), residues: 281 loop : -0.55 (0.27), residues: 488 *********************** 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 135 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.384 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.2585 time to fit residues: 49.1634 Evaluate side-chains 129 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1135 time to fit residues: 2.2309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12033 Z= 0.207 Angle : 0.498 7.458 16379 Z= 0.254 Chirality : 0.039 0.147 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.437 57.994 1670 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 0.24 % 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: 1.90 (0.22), residues: 1428 helix: 2.93 (0.19), residues: 660 sheet: 0.31 (0.30), residues: 286 loop : -0.54 (0.27), residues: 482 ********************** 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 137 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.438 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 135 average time/residue: 0.2547 time to fit residues: 49.8252 Evaluate side-chains 131 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1061 time to fit residues: 2.1284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** 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 = 0.3848 r_free = 0.3848 target = 0.172408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131612 restraints weight = 12366.093| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.31 r_work: 0.3045 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 12033 Z= 0.186 Angle : 0.493 8.939 16379 Z= 0.249 Chirality : 0.038 0.143 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.338 55.605 1670 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.63 % 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: 1.92 (0.22), residues: 1428 helix: 2.95 (0.19), residues: 659 sheet: 0.31 (0.30), residues: 286 loop : -0.52 (0.27), residues: 483 =============================================================================== Job complete usr+sys time: 2532.79 seconds wall clock time: 46 minutes 53.47 seconds (2813.47 seconds total)