Starting phenix.real_space_refine on Sat Apr 6 02:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/04_2024/8ggb_40001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/04_2024/8ggb_40001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/04_2024/8ggb_40001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/04_2024/8ggb_40001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/04_2024/8ggb_40001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/04_2024/8ggb_40001_updated.pdb" } resolution = 3.5 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= 0.020 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 37 5.16 5 C 4281 2.51 5 N 1204 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "R PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2234 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2462 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 352 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 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: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1680 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 455 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 216 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: 0.62 Number of scatterers: 6775 At special positions: 0 Unit cell: (84.1669, 135.361, 100.653, 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 37 16.00 P 3 15.00 O 1250 8.00 N 1204 7.00 C 4281 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 8 sheets defined 44.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.687A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.547A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 removed outlier: 3.571A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.514A pdb=" N ALA A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.067A pdb=" N GLN A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 177 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 4.093A 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 removed outlier: 3.559A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) 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: 3.511A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.680A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 392 removed outlier: 3.770A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.682A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (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 '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: 3.608A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 32 through 58 Processing helix chain 'R' and resid 69 through 85 Processing helix chain 'R' and resid 87 through 95 removed outlier: 3.781A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.355A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 removed outlier: 4.617A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 171 removed outlier: 3.679A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE R 166 " --> pdb=" O GLY R 162 " (cutoff:3.500A) removed outlier: 4.037A 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 181 through 186 Processing helix chain 'R' and resid 198 through 207 removed outlier: 3.591A pdb=" N VAL R 206 " --> pdb=" O SER R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.640A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.171A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.858A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 325 removed outlier: 4.020A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.510A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.671A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.520A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.537A 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: 4.344A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.891A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.768A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.952A 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: 3.619A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.781A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 861 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: 2.04 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1770 1.33 - 1.45: 1292 1.45 - 1.57: 3784 1.57 - 1.69: 6 1.69 - 1.81: 51 Bond restraints: 6903 Sorted by residual: bond pdb=" C PHE R 194 " pdb=" N THR R 195 " ideal model delta sigma weight residual 1.333 1.270 0.062 1.38e-02 5.25e+03 2.05e+01 bond pdb=" C PHE R 193 " pdb=" N PHE R 194 " ideal model delta sigma weight residual 1.331 1.277 0.054 1.28e-02 6.10e+03 1.79e+01 bond pdb=" C GLY R 50 " pdb=" O GLY R 50 " ideal model delta sigma weight residual 1.234 1.278 -0.045 1.21e-02 6.83e+03 1.36e+01 bond pdb=" N VAL R 34 " pdb=" CA VAL R 34 " ideal model delta sigma weight residual 1.461 1.503 -0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.30e-02 5.92e+03 1.14e+01 ... (remaining 6898 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 153 106.73 - 113.56: 3801 113.56 - 120.38: 2555 120.38 - 127.20: 2867 127.20 - 134.03: 71 Bond angle restraints: 9447 Sorted by residual: angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 104.36 6.92 1.09e+00 8.42e-01 4.02e+01 angle pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 111.28 104.52 6.76 1.09e+00 8.42e-01 3.84e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 105.31 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" C GLY R 50 " pdb=" N ASN R 51 " pdb=" CA ASN R 51 " ideal model delta sigma weight residual 120.28 113.15 7.13 1.34e+00 5.57e-01 2.83e+01 angle pdb=" C PHE R 194 " pdb=" CA PHE R 194 " pdb=" CB PHE R 194 " ideal model delta sigma weight residual 110.24 102.76 7.48 1.46e+00 4.69e-01 2.62e+01 ... (remaining 9442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.37: 3914 30.37 - 60.74: 92 60.74 - 91.12: 8 91.12 - 121.49: 3 121.49 - 151.86: 2 Dihedral angle restraints: 4019 sinusoidal: 1200 harmonic: 2819 Sorted by residual: dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -30.84 -151.86 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -161.19 -129.54 1 2.00e+01 2.50e-03 3.93e+01 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 -56.21 -175.84 119.64 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 878 0.053 - 0.106: 191 0.106 - 0.159: 43 0.159 - 0.212: 9 0.212 - 0.265: 6 Chirality restraints: 1127 Sorted by residual: chirality pdb=" CA ILE R 38 " pdb=" N ILE R 38 " pdb=" C ILE R 38 " pdb=" CB ILE R 38 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE R 47 " pdb=" N ILE R 47 " pdb=" C ILE R 47 " pdb=" CB ILE R 47 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1124 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 48 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C VAL R 48 " 0.068 2.00e-02 2.50e+03 pdb=" O VAL R 48 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE R 49 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 26 " 0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE A 26 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE A 26 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 27 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 35 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C GLY R 35 " 0.059 2.00e-02 2.50e+03 pdb=" O GLY R 35 " -0.022 2.00e-02 2.50e+03 pdb=" N MET R 36 " -0.020 2.00e-02 2.50e+03 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2195 2.82 - 3.34: 6202 3.34 - 3.86: 10159 3.86 - 4.38: 11138 4.38 - 4.90: 20103 Nonbonded interactions: 49797 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.306 2.440 nonbonded pdb=" O CYS A 162 " pdb=" OH TYR A 169 " model vdw 2.329 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.356 2.520 nonbonded pdb=" O SER B 160 " pdb=" OG SER B 160 " model vdw 2.358 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.359 2.440 ... (remaining 49792 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 group one per residue 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.670 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.010 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.005 0.062 6903 Z= 0.355 Angle : 0.795 10.573 9447 Z= 0.524 Chirality : 0.051 0.265 1127 Planarity : 0.004 0.039 1214 Dihedral : 14.627 151.861 2181 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.18 % Allowed : 0.89 % Favored : 98.93 % 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: 0.27 (0.27), residues: 942 helix: 1.68 (0.26), residues: 405 sheet: -1.01 (0.44), residues: 157 loop : -0.90 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.001 PHE B 234 TYR 0.017 0.001 TYR A 177 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8190 (m-80) cc_final: 0.7975 (m-80) REVERT: R 172 HIS cc_start: 0.6287 (m90) cc_final: 0.5972 (t-170) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1657 time to fit residues: 22.6124 Evaluate side-chains 87 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN G 18 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6903 Z= 0.281 Angle : 0.525 7.109 9447 Z= 0.280 Chirality : 0.044 0.150 1127 Planarity : 0.004 0.040 1214 Dihedral : 8.983 130.977 1049 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 9.82 % Favored : 88.57 % 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: 0.20 (0.27), residues: 942 helix: 1.64 (0.26), residues: 415 sheet: -1.05 (0.41), residues: 167 loop : -1.04 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.029 0.002 PHE B 234 TYR 0.013 0.001 TYR B 105 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.799 Fit side-chains REVERT: R 215 MET cc_start: 0.6269 (mtp) cc_final: 0.6064 (mtp) REVERT: R 332 PHE cc_start: 0.6836 (t80) cc_final: 0.6430 (t80) outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 0.1672 time to fit residues: 21.3848 Evaluate side-chains 87 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 281 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6903 Z= 0.152 Angle : 0.445 6.885 9447 Z= 0.233 Chirality : 0.041 0.160 1127 Planarity : 0.003 0.033 1214 Dihedral : 7.972 130.638 1049 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.61 % Allowed : 12.68 % Favored : 85.71 % 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: 942 helix: 1.89 (0.26), residues: 415 sheet: -0.97 (0.42), residues: 166 loop : -0.99 (0.29), residues: 361 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 B 234 TYR 0.014 0.001 TYR A 177 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.800 Fit side-chains REVERT: G 18 GLN cc_start: 0.8515 (tp40) cc_final: 0.8304 (tp-100) REVERT: R 332 PHE cc_start: 0.6849 (t80) cc_final: 0.6445 (t80) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.1652 time to fit residues: 21.1345 Evaluate side-chains 85 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 6903 Z= 0.140 Angle : 0.435 6.746 9447 Z= 0.225 Chirality : 0.041 0.165 1127 Planarity : 0.003 0.031 1214 Dihedral : 7.303 131.576 1049 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 14.46 % Favored : 83.39 % 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: 0.63 (0.28), residues: 942 helix: 2.08 (0.26), residues: 415 sheet: -0.82 (0.42), residues: 168 loop : -0.91 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.010 0.001 PHE B 241 TYR 0.005 0.001 TYR A 339 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.787 Fit side-chains REVERT: G 18 GLN cc_start: 0.8481 (tp40) cc_final: 0.8275 (tp-100) outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.1760 time to fit residues: 21.7158 Evaluate side-chains 91 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6903 Z= 0.149 Angle : 0.433 6.758 9447 Z= 0.224 Chirality : 0.041 0.171 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.210 134.109 1049 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.96 % Allowed : 16.43 % Favored : 81.61 % 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: 0.74 (0.28), residues: 942 helix: 2.12 (0.26), residues: 415 sheet: -0.69 (0.42), residues: 168 loop : -0.84 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE R 289 TYR 0.014 0.001 TYR A 177 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.798 Fit side-chains REVERT: G 18 GLN cc_start: 0.8574 (tp40) cc_final: 0.8347 (tp-100) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.1699 time to fit residues: 21.2438 Evaluate side-chains 90 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6903 Z= 0.151 Angle : 0.435 6.702 9447 Z= 0.225 Chirality : 0.041 0.208 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.189 135.909 1049 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.50 % Allowed : 17.14 % Favored : 80.36 % 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: 0.78 (0.28), residues: 942 helix: 2.18 (0.26), residues: 414 sheet: -0.59 (0.44), residues: 158 loop : -0.90 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR A 339 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.774 Fit side-chains REVERT: G 18 GLN cc_start: 0.8567 (tp40) cc_final: 0.8326 (tp-100) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.1713 time to fit residues: 22.4139 Evaluate side-chains 91 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 6903 Z= 0.132 Angle : 0.431 7.148 9447 Z= 0.224 Chirality : 0.041 0.188 1127 Planarity : 0.002 0.030 1214 Dihedral : 7.145 136.858 1049 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.32 % Allowed : 17.32 % Favored : 80.36 % 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: 0.79 (0.28), residues: 942 helix: 2.20 (0.27), residues: 410 sheet: -0.52 (0.44), residues: 156 loop : -0.90 (0.29), residues: 376 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 R 289 TYR 0.015 0.001 TYR A 177 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.836 Fit side-chains REVERT: A 393 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7127 (mp) REVERT: G 18 GLN cc_start: 0.8556 (tp40) cc_final: 0.8309 (tp-100) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1633 time to fit residues: 20.9084 Evaluate side-chains 92 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6903 Z= 0.150 Angle : 0.438 7.523 9447 Z= 0.228 Chirality : 0.041 0.204 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.139 137.049 1049 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.32 % Allowed : 17.50 % Favored : 80.18 % 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: 0.81 (0.28), residues: 942 helix: 2.27 (0.27), residues: 405 sheet: -0.48 (0.44), residues: 158 loop : -0.92 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE R 289 TYR 0.015 0.001 TYR A 177 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.716 Fit side-chains REVERT: A 393 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7132 (mp) REVERT: G 18 GLN cc_start: 0.8565 (tp40) cc_final: 0.8311 (tp-100) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 0.1706 time to fit residues: 21.2261 Evaluate side-chains 93 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6903 Z= 0.166 Angle : 0.450 8.105 9447 Z= 0.234 Chirality : 0.042 0.243 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.143 137.018 1049 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.86 % Allowed : 16.96 % Favored : 80.18 % 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: 0.77 (0.28), residues: 942 helix: 2.26 (0.27), residues: 404 sheet: -0.55 (0.43), residues: 164 loop : -0.95 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE R 289 TYR 0.005 0.001 TYR A 339 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.755 Fit side-chains REVERT: A 393 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7126 (mp) REVERT: G 18 GLN cc_start: 0.8567 (tp40) cc_final: 0.8307 (tp-100) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.1698 time to fit residues: 21.1569 Evaluate side-chains 88 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6903 Z= 0.126 Angle : 0.439 8.095 9447 Z= 0.226 Chirality : 0.041 0.238 1127 Planarity : 0.002 0.030 1214 Dihedral : 7.062 138.890 1049 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.61 % Allowed : 18.21 % Favored : 80.18 % 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: 0.83 (0.28), residues: 942 helix: 2.29 (0.27), residues: 405 sheet: -0.44 (0.44), residues: 156 loop : -0.94 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.017 0.001 PHE R 289 TYR 0.016 0.001 TYR A 177 ARG 0.004 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.779 Fit side-chains REVERT: A 23 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7422 (t0) REVERT: A 393 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6984 (mp) REVERT: G 18 GLN cc_start: 0.8542 (tp40) cc_final: 0.8293 (tp-100) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.1665 time to fit residues: 20.5598 Evaluate side-chains 88 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.0060 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.2832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.146905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118373 restraints weight = 10354.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117336 restraints weight = 7479.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118604 restraints weight = 7066.942| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6903 Z= 0.162 Angle : 0.926 59.113 9447 Z= 0.560 Chirality : 0.042 0.328 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.074 138.915 1049 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.96 % Allowed : 17.68 % Favored : 80.36 % Cbeta Deviations : 0.11 % 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: 0.81 (0.28), residues: 942 helix: 2.25 (0.27), residues: 405 sheet: -0.44 (0.44), residues: 156 loop : -0.93 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.009 0.001 PHE B 241 TYR 0.008 0.001 TYR A 177 ARG 0.004 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.75 seconds wall clock time: 29 minutes 18.44 seconds (1758.44 seconds total)