Starting phenix.real_space_refine (version: dev) on Mon Dec 12 03:57:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6s_25726/12_2022/7t6s_25726_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6s_25726/12_2022/7t6s_25726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6s_25726/12_2022/7t6s_25726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6s_25726/12_2022/7t6s_25726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6s_25726/12_2022/7t6s_25726_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6s_25726/12_2022/7t6s_25726_updated.pdb" } resolution = 3.0 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= 0.011 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8906 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1778 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2373 Unusual residues: {'FUI': 1} Classifications: {'peptide': 298, 'undetermined': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284, None: 1} Not linked: pdbres="LEU R 317 " pdbres="FUI R 401 " Time building chain proxies: 5.72, per 1000 atoms: 0.64 Number of scatterers: 8906 At special positions: 0 Unit cell: (117.72, 115.56, 103.68, 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 1 17.00 S 63 16.00 O 1636 8.00 N 1504 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 3.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 14 sheets defined 33.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.544A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.506A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 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 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.011A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.693A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) 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 10 through 23 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.944A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) 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 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 24 through 26 No H-bonds generated for 'chain 'R' and resid 24 through 26' Processing helix chain 'R' and resid 28 through 53 Processing helix chain 'R' and resid 59 through 76 removed outlier: 3.512A pdb=" N THR R 75 " --> pdb=" O ASP R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 86 removed outlier: 3.881A pdb=" N SER R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 128 removed outlier: 3.560A pdb=" N HIS R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE R 103 " --> pdb=" O LYS R 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 114 " --> pdb=" O PHE R 110 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 135 No H-bonds generated for 'chain 'R' and resid 132 through 135' Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 163 removed outlier: 3.822A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 181 through 184 No H-bonds generated for 'chain 'R' and resid 181 through 184' Processing helix chain 'R' and resid 187 through 207 removed outlier: 3.637A pdb=" N ARG R 205 " --> pdb=" O ARG R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 removed outlier: 3.850A pdb=" N ILE R 228 " --> pdb=" O ILE R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 266 removed outlier: 3.935A pdb=" N PHE R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 278 through 302 removed outlier: 4.435A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.427A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.755A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.897A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.654A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.415A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.382A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.580A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 92 through 99 removed outlier: 6.269A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.540A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 156 through 159 Processing sheet with id= M, first strand: chain 'E' and resid 225 through 231 removed outlier: 6.094A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG E 180 " --> pdb=" O PRO E 185 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 164 through 168 361 hydrogen bonds defined for protein. 1038 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: 2.73 Time building geometry restraints manager: 3.86 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: 1430 1.30 - 1.43: 2465 1.43 - 1.56: 5111 1.56 - 1.68: 0 1.68 - 1.81: 93 Bond restraints: 9099 Sorted by residual: bond pdb=" C08 FUI R 401 " pdb=" N07 FUI R 401 " ideal model delta sigma weight residual 1.383 1.292 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C PRO C 49 " pdb=" O PRO C 49 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.04e+01 bond pdb=" C PHE R 110 " pdb=" O PHE R 110 " ideal model delta sigma weight residual 1.236 1.177 0.058 1.31e-02 5.83e+03 1.98e+01 bond pdb=" C PRO B 94 " pdb=" O PRO B 94 " ideal model delta sigma weight residual 1.235 1.201 0.034 7.90e-03 1.60e+04 1.86e+01 bond pdb=" C18 FUI R 401 " pdb=" N19 FUI R 401 " ideal model delta sigma weight residual 1.371 1.453 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.64: 178 105.64 - 112.87: 4691 112.87 - 120.10: 4222 120.10 - 127.34: 3152 127.34 - 134.57: 86 Bond angle restraints: 12329 Sorted by residual: angle pdb=" N LEU R 81 " pdb=" CA LEU R 81 " pdb=" C LEU R 81 " ideal model delta sigma weight residual 113.97 105.43 8.54 1.28e+00 6.10e-01 4.46e+01 angle pdb=" N GLY R 209 " pdb=" CA GLY R 209 " pdb=" C GLY R 209 " ideal model delta sigma weight residual 113.37 121.86 -8.49 1.34e+00 5.57e-01 4.02e+01 angle pdb=" N VAL B 315 " pdb=" CA VAL B 315 " pdb=" C VAL B 315 " ideal model delta sigma weight residual 109.58 101.51 8.07 1.29e+00 6.01e-01 3.91e+01 angle pdb=" N PHE R 110 " pdb=" CA PHE R 110 " pdb=" C PHE R 110 " ideal model delta sigma weight residual 113.18 106.19 6.99 1.21e+00 6.83e-01 3.33e+01 angle pdb=" N THR R 265 " pdb=" CA THR R 265 " pdb=" C THR R 265 " ideal model delta sigma weight residual 113.41 106.69 6.72 1.22e+00 6.72e-01 3.03e+01 ... (remaining 12324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4880 17.57 - 35.14: 419 35.14 - 52.71: 60 52.71 - 70.28: 14 70.28 - 87.84: 10 Dihedral angle restraints: 5383 sinusoidal: 2109 harmonic: 3274 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 170.64 -77.64 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" C ASN R 108 " pdb=" N ASN R 108 " pdb=" CA ASN R 108 " pdb=" CB ASN R 108 " ideal model delta harmonic sigma weight residual -122.60 -139.29 16.69 0 2.50e+00 1.60e-01 4.46e+01 dihedral pdb=" N ASN R 108 " pdb=" C ASN R 108 " pdb=" CA ASN R 108 " pdb=" CB ASN R 108 " ideal model delta harmonic sigma weight residual 122.80 136.20 -13.40 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 5380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1106 0.119 - 0.237: 271 0.237 - 0.356: 23 0.356 - 0.474: 2 0.474 - 0.593: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ASN R 108 " pdb=" N ASN R 108 " pdb=" C ASN R 108 " pdb=" CB ASN R 108 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" CA TRP R 254 " pdb=" N TRP R 254 " pdb=" C TRP R 254 " pdb=" CB TRP R 254 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1400 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 54 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS A 54 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS A 54 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 55 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 191 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ARG E 191 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG E 191 " 0.021 2.00e-02 2.50e+03 pdb=" N MET E 192 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 99 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS R 99 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS R 99 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU R 100 " 0.020 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1260 2.76 - 3.29: 8776 3.29 - 3.83: 14772 3.83 - 4.36: 19559 4.36 - 4.90: 32241 Nonbonded interactions: 76608 Sorted by model distance: nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.223 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.257 2.440 nonbonded pdb=" NH1 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 2.281 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.285 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.293 2.440 ... (remaining 76603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 63 5.16 5 Cl 1 4.86 5 C 5702 2.51 5 N 1504 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.500 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: 0.000 Extract box with map and model: 2.540 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 27.540 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.013 0.091 9099 Z= 0.846 Angle : 1.286 11.214 12329 Z= 0.916 Chirality : 0.096 0.593 1403 Planarity : 0.008 0.071 1549 Dihedral : 13.455 87.844 3267 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1120 helix: -0.26 (0.25), residues: 392 sheet: 0.30 (0.31), residues: 268 loop : -0.87 (0.27), residues: 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.120 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.9997 time to fit residues: 170.4290 Evaluate side-chains 125 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 113 GLN E 183 GLN E 186 GLN R 102 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9099 Z= 0.231 Angle : 0.575 9.418 12329 Z= 0.301 Chirality : 0.043 0.142 1403 Planarity : 0.004 0.052 1549 Dihedral : 5.459 50.680 1248 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1120 helix: -0.02 (0.25), residues: 410 sheet: 0.19 (0.31), residues: 275 loop : -0.84 (0.28), residues: 435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.047 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 146 average time/residue: 0.9597 time to fit residues: 151.8972 Evaluate side-chains 132 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1005 time to fit residues: 1.7904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 82 GLN R 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 9099 Z= 0.306 Angle : 0.599 8.293 12329 Z= 0.311 Chirality : 0.044 0.167 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.498 48.701 1248 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.55 (0.24), residues: 1120 helix: 0.10 (0.26), residues: 408 sheet: 0.00 (0.30), residues: 278 loop : -0.92 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.060 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 144 average time/residue: 0.9948 time to fit residues: 155.6549 Evaluate side-chains 135 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.0953 time to fit residues: 2.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 113 GLN R 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 9099 Z= 0.263 Angle : 0.566 10.880 12329 Z= 0.292 Chirality : 0.043 0.171 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.412 48.932 1248 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1120 helix: 0.22 (0.26), residues: 408 sheet: -0.08 (0.30), residues: 270 loop : -0.88 (0.28), residues: 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.038 Fit side-chains outliers start: 35 outliers final: 15 residues processed: 151 average time/residue: 0.9631 time to fit residues: 157.5639 Evaluate side-chains 144 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.4274 time to fit residues: 4.3833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9099 Z= 0.226 Angle : 0.551 9.621 12329 Z= 0.282 Chirality : 0.043 0.144 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.278 48.619 1248 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.39 (0.25), residues: 1120 helix: 0.33 (0.26), residues: 409 sheet: -0.00 (0.31), residues: 266 loop : -0.85 (0.29), residues: 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.188 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 152 average time/residue: 0.9908 time to fit residues: 162.9215 Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.3454 time to fit residues: 3.9377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 9099 Z= 0.202 Angle : 0.527 9.335 12329 Z= 0.271 Chirality : 0.042 0.171 1403 Planarity : 0.004 0.039 1549 Dihedral : 5.172 48.385 1248 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.36 (0.25), residues: 1120 helix: 0.44 (0.26), residues: 408 sheet: -0.16 (0.30), residues: 272 loop : -0.80 (0.29), residues: 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.042 Fit side-chains outliers start: 32 outliers final: 18 residues processed: 153 average time/residue: 0.9856 time to fit residues: 163.3579 Evaluate side-chains 148 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 6 average time/residue: 0.1350 time to fit residues: 2.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 9099 Z= 0.189 Angle : 0.534 11.797 12329 Z= 0.270 Chirality : 0.042 0.184 1403 Planarity : 0.004 0.039 1549 Dihedral : 5.084 48.300 1248 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.29 (0.25), residues: 1120 helix: 0.47 (0.26), residues: 409 sheet: -0.07 (0.31), residues: 267 loop : -0.77 (0.29), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.090 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 151 average time/residue: 0.9624 time to fit residues: 157.6745 Evaluate side-chains 139 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.4852 time to fit residues: 3.1156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 9099 Z= 0.314 Angle : 0.592 10.802 12329 Z= 0.303 Chirality : 0.044 0.237 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.350 48.391 1248 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.44 (0.25), residues: 1120 helix: 0.40 (0.26), residues: 410 sheet: -0.19 (0.30), residues: 270 loop : -0.88 (0.29), residues: 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 143 average time/residue: 0.9539 time to fit residues: 148.1920 Evaluate side-chains 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.3605 time to fit residues: 3.5469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 9099 Z= 0.293 Angle : 0.590 10.917 12329 Z= 0.300 Chirality : 0.044 0.205 1403 Planarity : 0.004 0.041 1549 Dihedral : 5.355 48.243 1248 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.51 (0.25), residues: 1120 helix: 0.34 (0.26), residues: 407 sheet: -0.20 (0.30), residues: 270 loop : -0.94 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.985 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 139 average time/residue: 1.0310 time to fit residues: 155.3760 Evaluate side-chains 138 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.1102 time to fit residues: 1.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 9099 Z= 0.197 Angle : 0.546 11.688 12329 Z= 0.277 Chirality : 0.043 0.281 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.149 48.210 1248 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.37 (0.25), residues: 1120 helix: 0.41 (0.26), residues: 406 sheet: -0.05 (0.31), residues: 266 loop : -0.86 (0.29), residues: 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.068 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 141 average time/residue: 1.0185 time to fit residues: 155.2977 Evaluate side-chains 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0823 time to fit residues: 1.5991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109570 restraints weight = 10327.643| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.86 r_work: 0.2903 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 9099 Z= 0.197 Angle : 0.542 11.598 12329 Z= 0.277 Chirality : 0.043 0.249 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.101 47.996 1248 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.37 (0.25), residues: 1120 helix: 0.41 (0.26), residues: 407 sheet: -0.13 (0.31), residues: 273 loop : -0.80 (0.29), residues: 440 =============================================================================== Job complete usr+sys time: 3192.01 seconds wall clock time: 57 minutes 54.11 seconds (3474.11 seconds total)