Starting phenix.real_space_refine on Sat Apr 6 03:03:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg5_29995/04_2024/8gg5_29995_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg5_29995/04_2024/8gg5_29995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg5_29995/04_2024/8gg5_29995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg5_29995/04_2024/8gg5_29995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg5_29995/04_2024/8gg5_29995_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg5_29995/04_2024/8gg5_29995_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 47 5.16 5 C 4351 2.51 5 N 1167 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" 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: 6799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1799 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2456 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 335 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2157 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 4.00, per 1000 atoms: 0.59 Number of scatterers: 6799 At special positions: 0 Unit cell: (85.0346, 133.626, 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 47 16.00 P 3 15.00 O 1231 8.00 N 1167 7.00 C 4351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 43.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.827A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.532A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 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: 3.556A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.753A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.596A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.682A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 23 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 34 through 60 removed outlier: 3.702A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 68 through 85 removed outlier: 3.720A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 104 through 136 removed outlier: 4.193A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.638A 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 147 through 170 removed outlier: 4.016A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.227A 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 179 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.629A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.676A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.677A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.441A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.622A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.071A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.892A 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 105 removed outlier: 7.111A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.838A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.610A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.898A 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: 3.778A 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: 6.713A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 897 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: 1.94 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2185 1.34 - 1.46: 1621 1.46 - 1.58: 3065 1.58 - 1.70: 5 1.70 - 1.81: 66 Bond restraints: 6942 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.435 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.563 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.318 0.035 2.00e-02 2.50e+03 3.14e+00 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 145 106.72 - 113.54: 3888 113.54 - 120.37: 2521 120.37 - 127.19: 2842 127.19 - 134.01: 79 Bond angle restraints: 9475 Sorted by residual: angle pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C4' GTP A 401 " ideal model delta sigma weight residual 111.00 103.45 7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" C PHE B 234 " ideal model delta sigma weight residual 110.50 113.78 -3.28 1.41e+00 5.03e-01 5.42e+00 angle pdb=" N LEU R 287 " pdb=" CA LEU R 287 " pdb=" C LEU R 287 " ideal model delta sigma weight residual 109.81 114.33 -4.52 2.21e+00 2.05e-01 4.19e+00 angle pdb=" C GLU A 330 " pdb=" CA GLU A 330 " pdb=" CB GLU A 330 " ideal model delta sigma weight residual 110.36 113.80 -3.44 1.78e+00 3.16e-01 3.74e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 122.96 -6.66 3.50e+00 8.16e-02 3.62e+00 ... (remaining 9470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 3976 34.79 - 69.58: 62 69.58 - 104.37: 5 104.37 - 139.16: 0 139.16 - 173.95: 1 Dihedral angle restraints: 4044 sinusoidal: 1409 harmonic: 2635 Sorted by residual: 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 86.93 173.95 1 2.00e+01 2.50e-03 4.79e+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 11.47 93.12 1 2.00e+01 2.50e-03 2.53e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 601 0.026 - 0.052: 290 0.052 - 0.078: 145 0.078 - 0.104: 51 0.104 - 0.130: 32 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1116 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO B 39 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 332 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 236 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1967 2.81 - 3.34: 5991 3.34 - 3.86: 10403 3.86 - 4.38: 11954 4.38 - 4.90: 22000 Nonbonded interactions: 52315 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.292 2.440 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.294 2.520 nonbonded pdb=" O TYR A 253 " pdb=" ND2 ASN A 264 " model vdw 2.314 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.323 2.520 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.336 2.440 ... (remaining 52310 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: 2.110 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: 7.720 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 22.080 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.051 6942 Z= 0.261 Angle : 0.516 7.549 9475 Z= 0.272 Chirality : 0.042 0.130 1119 Planarity : 0.004 0.041 1186 Dihedral : 14.022 173.947 2328 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 0.36 (0.28), residues: 890 helix: 1.46 (0.27), residues: 385 sheet: -0.52 (0.39), residues: 166 loop : -0.71 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.006 0.001 HIS B 62 PHE 0.014 0.002 PHE R 49 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.802 Fit side-chains REVERT: A 27 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8339 (mt-10) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2034 time to fit residues: 23.4584 Evaluate side-chains 73 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6942 Z= 0.168 Angle : 0.466 7.380 9475 Z= 0.247 Chirality : 0.041 0.140 1119 Planarity : 0.003 0.036 1186 Dihedral : 7.394 173.022 993 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.75 % Allowed : 6.91 % Favored : 92.34 % 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: 0.70 (0.28), residues: 890 helix: 1.73 (0.27), residues: 388 sheet: -0.07 (0.41), residues: 167 loop : -0.72 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE B 151 TYR 0.007 0.001 TYR B 105 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.814 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 0.1823 time to fit residues: 20.7229 Evaluate side-chains 79 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6942 Z= 0.285 Angle : 0.520 7.713 9475 Z= 0.275 Chirality : 0.043 0.138 1119 Planarity : 0.004 0.037 1186 Dihedral : 7.563 175.263 993 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.05 % Allowed : 11.41 % Favored : 87.54 % 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: 890 helix: 1.63 (0.27), residues: 384 sheet: 0.02 (0.40), residues: 172 loop : -0.75 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE R 282 TYR 0.011 0.001 TYR B 111 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.766 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.1993 time to fit residues: 20.5571 Evaluate side-chains 76 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6942 Z= 0.113 Angle : 0.420 7.234 9475 Z= 0.222 Chirality : 0.039 0.132 1119 Planarity : 0.003 0.035 1186 Dihedral : 7.239 172.500 993 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.75 % Allowed : 14.71 % Favored : 84.53 % 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: 0.98 (0.28), residues: 890 helix: 1.96 (0.27), residues: 385 sheet: 0.24 (0.41), residues: 171 loop : -0.67 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.778 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 0.1896 time to fit residues: 21.1129 Evaluate side-chains 77 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6942 Z= 0.260 Angle : 0.501 7.592 9475 Z= 0.265 Chirality : 0.042 0.135 1119 Planarity : 0.003 0.036 1186 Dihedral : 7.430 174.397 993 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.90 % Allowed : 15.62 % Favored : 83.48 % 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: 0.82 (0.28), residues: 890 helix: 1.79 (0.26), residues: 385 sheet: 0.12 (0.41), residues: 171 loop : -0.68 (0.32), residues: 334 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 0.013 0.002 PHE R 282 TYR 0.012 0.001 TYR B 111 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.811 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.1951 time to fit residues: 21.7355 Evaluate side-chains 80 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.0060 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5574 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6942 Z= 0.139 Angle : 0.433 7.364 9475 Z= 0.230 Chirality : 0.040 0.132 1119 Planarity : 0.003 0.035 1186 Dihedral : 7.279 173.251 993 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.75 % Allowed : 16.67 % 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: 1.01 (0.28), residues: 890 helix: 2.00 (0.26), residues: 385 sheet: 0.25 (0.41), residues: 173 loop : -0.66 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.014 0.001 TYR B 111 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.716 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.2002 time to fit residues: 21.3008 Evaluate side-chains 78 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 53 optimal weight: 0.0040 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- 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: 0.8322 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6942 Z= 0.106 Angle : 0.404 7.144 9475 Z= 0.214 Chirality : 0.039 0.132 1119 Planarity : 0.003 0.034 1186 Dihedral : 7.102 171.229 993 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.90 % Allowed : 16.37 % Favored : 82.73 % 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: 1.24 (0.28), residues: 890 helix: 2.21 (0.26), residues: 387 sheet: 0.38 (0.41), residues: 170 loop : -0.59 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE R 49 TYR 0.013 0.001 TYR B 111 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.747 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.1892 time to fit residues: 21.2308 Evaluate side-chains 77 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 182 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6942 Z= 0.134 Angle : 0.417 7.225 9475 Z= 0.221 Chirality : 0.040 0.132 1119 Planarity : 0.003 0.033 1186 Dihedral : 7.125 171.791 993 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.90 % Allowed : 16.37 % Favored : 82.73 % 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: 1.24 (0.28), residues: 890 helix: 2.25 (0.26), residues: 386 sheet: 0.34 (0.41), residues: 171 loop : -0.60 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.013 0.001 TYR B 111 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.727 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 77 average time/residue: 0.1901 time to fit residues: 19.9485 Evaluate side-chains 78 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 182 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6942 Z= 0.194 Angle : 0.455 7.434 9475 Z= 0.241 Chirality : 0.041 0.133 1119 Planarity : 0.003 0.034 1186 Dihedral : 7.269 173.366 993 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.05 % Allowed : 16.37 % 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: 1.13 (0.28), residues: 890 helix: 2.13 (0.26), residues: 387 sheet: 0.28 (0.41), residues: 171 loop : -0.63 (0.33), residues: 332 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 0.011 0.001 PHE R 282 TYR 0.014 0.001 TYR B 111 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.804 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.1877 time to fit residues: 19.4510 Evaluate side-chains 77 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6942 Z= 0.168 Angle : 0.438 7.380 9475 Z= 0.232 Chirality : 0.040 0.132 1119 Planarity : 0.003 0.034 1186 Dihedral : 7.251 173.092 993 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.90 % Allowed : 16.37 % Favored : 82.73 % 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: 1.16 (0.28), residues: 890 helix: 2.16 (0.26), residues: 388 sheet: 0.28 (0.40), residues: 171 loop : -0.62 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE R 49 TYR 0.014 0.001 TYR B 111 ARG 0.004 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.807 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.1874 time to fit residues: 19.4667 Evaluate side-chains 78 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.145035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115057 restraints weight = 8634.487| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.09 r_work: 0.3003 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6942 Z= 0.146 Angle : 0.424 7.301 9475 Z= 0.225 Chirality : 0.040 0.133 1119 Planarity : 0.003 0.034 1186 Dihedral : 7.201 172.493 993 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.05 % Allowed : 16.37 % 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: 1.24 (0.28), residues: 890 helix: 2.24 (0.26), residues: 388 sheet: 0.30 (0.40), residues: 171 loop : -0.61 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.015 0.001 TYR B 111 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.27 seconds wall clock time: 32 minutes 35.27 seconds (1955.27 seconds total)