Starting phenix.real_space_refine on Sat Apr 6 00:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/04_2024/8ggc_40002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/04_2024/8ggc_40002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/04_2024/8ggc_40002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/04_2024/8ggc_40002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/04_2024/8ggc_40002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/04_2024/8ggc_40002_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 P 3 5.49 5 S 38 5.16 5 C 4112 2.51 5 N 1152 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2123 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2452 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 348 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1545 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 616 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 222 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.65 Number of scatterers: 6515 At special positions: 0 Unit cell: (84.1669, 136.229, 98.9178, 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) S 38 16.00 P 3 15.00 O 1210 8.00 N 1152 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 8 sheets defined 41.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.570A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.506A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.530A pdb=" N LEU A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 176 through 179 No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 196 through 199 No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.830A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.604A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.723A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.835A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.515A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.855A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.622A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 32 through 54 removed outlier: 3.507A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 94 removed outlier: 3.976A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.877A pdb=" N ALA R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.747A pdb=" N ASP R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 152 through 171 removed outlier: 3.763A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 199 through 207 Processing helix chain 'R' and resid 209 through 234 removed outlier: 3.502A pdb=" N VAL R 216 " --> pdb=" O LEU R 212 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.353A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.099A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 321 removed outlier: 3.792A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.153A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.896A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.028A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.361A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.575A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.908A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.683A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 4.453A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 810 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: 1.77 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1094 1.32 - 1.44: 1819 1.44 - 1.57: 3662 1.57 - 1.69: 6 1.69 - 1.81: 52 Bond restraints: 6633 Sorted by residual: bond pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 1.521 1.446 0.075 1.21e-02 6.83e+03 3.85e+01 bond pdb=" CA TYR A 391 " pdb=" C TYR A 391 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.30e-02 5.92e+03 2.81e+01 bond pdb=" N LEU A 393 " pdb=" CA LEU A 393 " ideal model delta sigma weight residual 1.456 1.397 0.060 1.28e-02 6.10e+03 2.19e+01 bond pdb=" N GLU A 392 " pdb=" CA GLU A 392 " ideal model delta sigma weight residual 1.456 1.413 0.042 1.23e-02 6.61e+03 1.19e+01 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.586 -0.063 2.00e-02 2.50e+03 9.88e+00 ... (remaining 6628 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.61: 90 105.61 - 112.72: 3550 112.72 - 119.82: 2009 119.82 - 126.93: 3344 126.93 - 134.03: 75 Bond angle restraints: 9068 Sorted by residual: angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.28 121.54 -10.26 1.09e+00 8.42e-01 8.85e+01 angle pdb=" N LEU A 393 " pdb=" CA LEU A 393 " pdb=" C LEU A 393 " ideal model delta sigma weight residual 110.10 98.51 11.59 1.49e+00 4.50e-01 6.05e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 108.79 99.59 9.20 1.53e+00 4.27e-01 3.62e+01 angle pdb=" N PRO R 138 " pdb=" CA PRO R 138 " pdb=" C PRO R 138 " ideal model delta sigma weight residual 113.53 121.74 -8.21 1.39e+00 5.18e-01 3.49e+01 angle pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 122.68 114.35 8.33 1.47e+00 4.63e-01 3.21e+01 ... (remaining 9063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.35: 3751 29.35 - 58.71: 95 58.71 - 88.06: 5 88.06 - 117.42: 4 117.42 - 146.77: 2 Dihedral angle restraints: 3857 sinusoidal: 1143 harmonic: 2714 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 157.02 146.77 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -15.68 120.28 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 146.58 114.29 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 3854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 876 0.055 - 0.109: 165 0.109 - 0.164: 27 0.164 - 0.219: 9 0.219 - 0.273: 3 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1077 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ASP A 223 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP A 223 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 224 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 225 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLY A 225 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 225 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 226 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 324 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ALA A 324 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 324 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 325 " -0.013 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1459 2.78 - 3.31: 5936 3.31 - 3.84: 9846 3.84 - 4.37: 10663 4.37 - 4.90: 19418 Nonbonded interactions: 47322 Sorted by model distance: nonbonded pdb=" CD1 ILE A 207 " pdb=" O ASP A 223 " model vdw 2.250 3.460 nonbonded pdb=" O CYS A 162 " pdb=" OH TYR A 169 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.293 2.440 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.299 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.315 2.440 ... (remaining 47317 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 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: 2.250 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: 8.750 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 22.210 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6633 Z= 0.285 Angle : 0.731 11.592 9068 Z= 0.424 Chirality : 0.046 0.273 1080 Planarity : 0.004 0.040 1167 Dihedral : 14.244 146.773 2087 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.19 % Allowed : 1.12 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.28), residues: 904 helix: 1.58 (0.26), residues: 377 sheet: -0.76 (0.41), residues: 176 loop : -1.36 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.004 0.001 HIS A 387 PHE 0.011 0.001 PHE A 208 TYR 0.016 0.001 TYR R 316 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.743 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1775 time to fit residues: 23.2711 Evaluate side-chains 82 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6633 Z= 0.177 Angle : 0.482 7.655 9068 Z= 0.256 Chirality : 0.041 0.150 1080 Planarity : 0.003 0.033 1167 Dihedral : 8.458 120.545 1011 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.69 % Allowed : 8.99 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.28), residues: 904 helix: 1.98 (0.26), residues: 393 sheet: -0.57 (0.44), residues: 159 loop : -1.29 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 376 TYR 0.012 0.001 TYR A 360 ARG 0.008 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.785 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.1456 time to fit residues: 19.2797 Evaluate side-chains 87 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 213 GLN A 292 ASN B 88 ASN B 220 GLN R 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6633 Z= 0.208 Angle : 0.475 8.606 9068 Z= 0.250 Chirality : 0.041 0.144 1080 Planarity : 0.003 0.036 1167 Dihedral : 7.672 108.855 1009 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.81 % Allowed : 14.61 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.29), residues: 904 helix: 2.18 (0.27), residues: 393 sheet: -0.64 (0.43), residues: 165 loop : -1.27 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.007 0.001 HIS B 142 PHE 0.016 0.001 PHE A 376 TYR 0.015 0.001 TYR A 360 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.699 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.1436 time to fit residues: 19.8723 Evaluate side-chains 88 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 213 GLN A 292 ASN B 88 ASN R 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6633 Z= 0.162 Angle : 0.446 8.391 9068 Z= 0.233 Chirality : 0.040 0.131 1080 Planarity : 0.003 0.035 1167 Dihedral : 7.298 106.733 1009 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.06 % Allowed : 17.04 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 904 helix: 2.22 (0.27), residues: 394 sheet: -0.59 (0.44), residues: 159 loop : -1.28 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.006 0.001 HIS B 225 PHE 0.015 0.001 PHE A 376 TYR 0.012 0.001 TYR A 360 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.769 Fit side-chains REVERT: G 18 GLN cc_start: 0.8988 (tt0) cc_final: 0.8764 (tt0) outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 0.1627 time to fit residues: 20.9015 Evaluate side-chains 89 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 292 ASN B 88 ASN B 142 HIS ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6633 Z= 0.231 Angle : 0.475 8.921 9068 Z= 0.249 Chirality : 0.041 0.145 1080 Planarity : 0.003 0.036 1167 Dihedral : 7.228 107.071 1009 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.81 % Allowed : 17.98 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.29), residues: 904 helix: 2.22 (0.27), residues: 394 sheet: -0.60 (0.43), residues: 162 loop : -1.30 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.007 0.001 HIS B 142 PHE 0.016 0.002 PHE B 241 TYR 0.014 0.001 TYR A 360 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.749 Fit side-chains REVERT: G 18 GLN cc_start: 0.9014 (tt0) cc_final: 0.8809 (tt0) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.1449 time to fit residues: 18.7258 Evaluate side-chains 88 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 0.0170 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 213 GLN A 292 ASN B 88 ASN ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6633 Z= 0.180 Angle : 0.460 9.308 9068 Z= 0.240 Chirality : 0.041 0.127 1080 Planarity : 0.003 0.035 1167 Dihedral : 7.061 106.817 1009 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.00 % Allowed : 18.35 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 904 helix: 2.25 (0.27), residues: 394 sheet: -0.59 (0.42), residues: 162 loop : -1.28 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.007 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.014 0.001 TYR A 360 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.764 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.1639 time to fit residues: 20.8168 Evaluate side-chains 91 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 292 ASN B 88 ASN B 142 HIS ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6633 Z= 0.153 Angle : 0.446 8.962 9068 Z= 0.231 Chirality : 0.040 0.128 1080 Planarity : 0.003 0.033 1167 Dihedral : 6.888 104.799 1009 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.81 % Allowed : 19.29 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.29), residues: 904 helix: 2.27 (0.27), residues: 395 sheet: -0.53 (0.43), residues: 158 loop : -1.26 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.006 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.013 0.001 TYR A 360 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.708 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 91 average time/residue: 0.1549 time to fit residues: 19.7454 Evaluate side-chains 88 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 292 ASN B 88 ASN B 142 HIS ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6633 Z= 0.154 Angle : 0.451 8.897 9068 Z= 0.232 Chirality : 0.040 0.129 1080 Planarity : 0.003 0.036 1167 Dihedral : 6.756 103.061 1009 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.81 % Allowed : 19.10 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.29), residues: 904 helix: 2.30 (0.27), residues: 395 sheet: -0.53 (0.43), residues: 156 loop : -1.27 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.013 0.001 TYR A 360 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.754 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 92 average time/residue: 0.1569 time to fit residues: 20.2124 Evaluate side-chains 92 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 292 ASN B 88 ASN B 142 HIS ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6633 Z= 0.152 Angle : 0.456 8.814 9068 Z= 0.233 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.038 1167 Dihedral : 6.659 102.482 1009 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.81 % Allowed : 19.85 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.29), residues: 904 helix: 2.34 (0.27), residues: 395 sheet: -0.52 (0.43), residues: 156 loop : -1.26 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 376 TYR 0.013 0.001 TYR A 360 ARG 0.009 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.750 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 92 average time/residue: 0.1640 time to fit residues: 21.0003 Evaluate side-chains 91 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 292 ASN B 142 HIS R 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6633 Z= 0.200 Angle : 0.472 9.215 9068 Z= 0.243 Chirality : 0.041 0.130 1080 Planarity : 0.003 0.040 1167 Dihedral : 6.650 102.745 1009 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.18 % Allowed : 19.66 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 904 helix: 2.32 (0.27), residues: 395 sheet: -0.47 (0.43), residues: 156 loop : -1.27 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 339 HIS 0.007 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.014 0.001 TYR A 360 ARG 0.009 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.765 Fit side-chains REVERT: A 209 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7899 (mt-10) outliers start: 17 outliers final: 15 residues processed: 92 average time/residue: 0.1623 time to fit residues: 20.8399 Evaluate side-chains 94 residues out of total 810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 292 ASN B 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118320 restraints weight = 10001.562| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.66 r_work: 0.3444 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6633 Z= 0.152 Angle : 0.460 8.859 9068 Z= 0.235 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.040 1167 Dihedral : 6.480 102.177 1009 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.81 % Allowed : 19.85 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.29), residues: 904 helix: 2.35 (0.27), residues: 395 sheet: -0.51 (0.43), residues: 156 loop : -1.25 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.002 0.001 HIS B 183 PHE 0.015 0.001 PHE A 376 TYR 0.013 0.001 TYR A 360 ARG 0.009 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.31 seconds wall clock time: 31 minutes 45.20 seconds (1905.20 seconds total)