Starting phenix.real_space_refine on Tue Mar 11 21:50:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unq_42413/03_2025/8unq_42413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unq_42413/03_2025/8unq_42413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unq_42413/03_2025/8unq_42413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unq_42413/03_2025/8unq_42413.map" model { file = "/net/cci-nas-00/data/ceres_data/8unq_42413/03_2025/8unq_42413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unq_42413/03_2025/8unq_42413.cif" } resolution = 3.3 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= 0.025 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 40 5.16 5 C 4289 2.51 5 N 1161 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6687 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1770 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 239, 1758 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 239, 1758 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 1778 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2412 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 120 Chain: "G" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 343 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2114 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 122 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.82, per 1000 atoms: 0.87 Number of scatterers: 6687 At special positions: 0 Unit cell: (85.9023, 135.361, 98.0501, 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 40 16.00 P 3 15.00 O 1194 8.00 N 1161 7.00 C 4289 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 - 3.00 Amino acid : True - 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: 1.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 48.4% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.565A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.517A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.582A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.730A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.143A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.542A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.568A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.518A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.702A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.507A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.578A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.525A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.266A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.114A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 163 removed outlier: 3.891A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.771A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.831A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.747A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.541A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.596A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.521A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.677A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.619A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.193A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.935A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.042A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.882A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.512A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.827A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1032 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: 1.95 Time building geometry restraints manager: 2.13 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: 1418 1.33 - 1.45: 1637 1.45 - 1.58: 3717 1.58 - 1.70: 5 1.70 - 1.82: 54 Bond restraints: 6831 Sorted by residual: bond pdb=" CA SER A 51 " pdb=" CB SER A 51 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.59e-02 3.96e+03 1.20e+01 bond pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 1.459 1.500 -0.042 1.32e-02 5.74e+03 9.94e+00 bond pdb=" CA ALA R 271 " pdb=" CB ALA R 271 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.55e-02 4.16e+03 8.65e+00 bond pdb=" N LYS A 58 " pdb=" CA LYS A 58 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.53e+00 bond pdb=" CA SER A 54 " pdb=" CB SER A 54 " ideal model delta sigma weight residual 1.528 1.485 0.044 1.56e-02 4.11e+03 7.88e+00 ... (remaining 6826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 9109 2.30 - 4.60: 209 4.60 - 6.91: 19 6.91 - 9.21: 7 9.21 - 11.51: 4 Bond angle restraints: 9348 Sorted by residual: angle pdb=" N ALA G 12 " pdb=" CA ALA G 12 " pdb=" C ALA G 12 " ideal model delta sigma weight residual 111.28 104.30 6.98 1.09e+00 8.42e-01 4.10e+01 angle pdb=" N LEU G 19 " pdb=" CA LEU G 19 " pdb=" C LEU G 19 " ideal model delta sigma weight residual 111.28 105.10 6.18 1.09e+00 8.42e-01 3.22e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 110.62 105.19 5.43 1.02e+00 9.61e-01 2.84e+01 angle pdb=" N LEU B 7 " pdb=" CA LEU B 7 " pdb=" C LEU B 7 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 angle pdb=" N LEU B 4 " pdb=" CA LEU B 4 " pdb=" C LEU B 4 " ideal model delta sigma weight residual 111.28 106.37 4.91 1.09e+00 8.42e-01 2.03e+01 ... (remaining 9343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 3857 31.64 - 63.29: 90 63.29 - 94.93: 3 94.93 - 126.57: 1 126.57 - 158.21: 1 Dihedral angle restraints: 3952 sinusoidal: 1276 harmonic: 2676 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 154.11 -61.11 1 1.00e+01 1.00e-02 4.96e+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 -132.52 -158.21 1 2.00e+01 2.50e-03 4.63e+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 -5.32 109.91 1 2.00e+01 2.50e-03 3.22e+01 ... (remaining 3949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 810 0.044 - 0.089: 212 0.089 - 0.133: 75 0.133 - 0.177: 14 0.177 - 0.222: 8 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA VAL A 256 " pdb=" N VAL A 256 " pdb=" C VAL A 256 " pdb=" CB VAL A 256 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU B 7 " pdb=" N LEU B 7 " pdb=" C LEU B 7 " pdb=" CB LEU B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1116 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 17 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C LYS A 17 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 17 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 18 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 53 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C LYS A 53 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS A 53 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 54 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 7 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C LEU B 7 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU B 7 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B 8 " -0.012 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 804 2.75 - 3.29: 6422 3.29 - 3.83: 10435 3.83 - 4.36: 11471 4.36 - 4.90: 21280 Nonbonded interactions: 50412 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.352 3.120 nonbonded pdb=" OD1 ASP A 295 " pdb=" N LEU A 296 " model vdw 2.352 3.120 ... (remaining 50407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.49 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: 1.550 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.580 Find NCS groups from input model: 0.090 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 0.055 6831 Z= 0.316 Angle : 0.766 11.509 9348 Z= 0.506 Chirality : 0.049 0.222 1119 Planarity : 0.004 0.051 1172 Dihedral : 13.493 158.212 2208 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.33 % Allowed : 0.99 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 902 helix: 2.20 (0.27), residues: 397 sheet: 0.32 (0.42), residues: 166 loop : -0.87 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 105 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.747 Fit side-chains REVERT: B 78 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8173 (mttp) REVERT: G 38 MET cc_start: 0.8235 (tpp) cc_final: 0.7914 (mtp) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2042 time to fit residues: 29.6565 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100840 restraints weight = 30055.230| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.33 r_work: 0.3130 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6831 Z= 0.252 Angle : 0.530 6.976 9348 Z= 0.285 Chirality : 0.042 0.160 1119 Planarity : 0.003 0.040 1172 Dihedral : 7.546 145.747 1007 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.66 % Allowed : 9.03 % Favored : 90.31 % 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: 1.12 (0.29), residues: 902 helix: 2.28 (0.27), residues: 401 sheet: 0.17 (0.42), residues: 162 loop : -0.88 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 PHE 0.015 0.001 PHE B 241 TYR 0.014 0.001 TYR A 339 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.785 Fit side-chains REVERT: G 38 MET cc_start: 0.8584 (tpp) cc_final: 0.8233 (mtp) outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.2064 time to fit residues: 25.0153 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 12 optimal weight: 0.0050 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106436 restraints weight = 24630.425| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.89 r_work: 0.3227 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6831 Z= 0.121 Angle : 0.436 6.299 9348 Z= 0.235 Chirality : 0.039 0.140 1119 Planarity : 0.003 0.036 1172 Dihedral : 7.144 146.691 1005 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.33 % Allowed : 11.49 % Favored : 88.18 % 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: 1.39 (0.29), residues: 902 helix: 2.58 (0.27), residues: 401 sheet: 0.31 (0.42), residues: 160 loop : -0.84 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.764 Fit side-chains REVERT: B 59 TYR cc_start: 0.8361 (m-80) cc_final: 0.8073 (m-80) REVERT: G 38 MET cc_start: 0.8456 (tpp) cc_final: 0.8148 (mtp) outliers start: 2 outliers final: 1 residues processed: 98 average time/residue: 0.1980 time to fit residues: 25.9355 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103142 restraints weight = 28576.094| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.35 r_work: 0.3165 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6831 Z= 0.201 Angle : 0.470 6.393 9348 Z= 0.252 Chirality : 0.040 0.152 1119 Planarity : 0.003 0.038 1172 Dihedral : 7.153 145.287 1005 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.99 % Allowed : 12.32 % Favored : 86.70 % 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: 1.43 (0.29), residues: 902 helix: 2.57 (0.27), residues: 406 sheet: 0.14 (0.41), residues: 162 loop : -0.69 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 241 TYR 0.012 0.001 TYR R 308 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.830 Fit side-chains REVERT: B 59 TYR cc_start: 0.8555 (m-80) cc_final: 0.6967 (m-80) REVERT: G 38 MET cc_start: 0.8546 (tpp) cc_final: 0.8208 (mtp) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.2039 time to fit residues: 25.9559 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098261 restraints weight = 41324.346| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 5.17 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6831 Z= 0.263 Angle : 0.505 6.366 9348 Z= 0.273 Chirality : 0.041 0.153 1119 Planarity : 0.003 0.039 1172 Dihedral : 7.258 142.866 1005 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 12.15 % Favored : 86.54 % 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: 1.29 (0.29), residues: 902 helix: 2.44 (0.27), residues: 412 sheet: -0.09 (0.40), residues: 162 loop : -0.70 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE B 241 TYR 0.014 0.001 TYR R 308 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.778 Fit side-chains REVERT: B 234 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7495 (t80) REVERT: G 38 MET cc_start: 0.7856 (tpp) cc_final: 0.7444 (mtp) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 0.2072 time to fit residues: 25.4852 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104204 restraints weight = 36407.055| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.78 r_work: 0.3085 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6831 Z= 0.128 Angle : 0.434 6.284 9348 Z= 0.234 Chirality : 0.039 0.137 1119 Planarity : 0.003 0.038 1172 Dihedral : 7.002 144.164 1005 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.66 % Allowed : 13.14 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 902 helix: 2.65 (0.27), residues: 404 sheet: 0.10 (0.42), residues: 160 loop : -0.74 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR R 185 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.722 Fit side-chains REVERT: G 38 MET cc_start: 0.8521 (tpp) cc_final: 0.8166 (mtp) REVERT: R 231 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8472 (tm-30) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.2001 time to fit residues: 25.0579 Evaluate side-chains 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.0370 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107969 restraints weight = 39310.442| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.92 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6831 Z= 0.103 Angle : 0.415 6.423 9348 Z= 0.222 Chirality : 0.038 0.136 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.845 145.682 1005 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.33 % Allowed : 13.63 % Favored : 86.04 % 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: 1.62 (0.29), residues: 902 helix: 2.81 (0.27), residues: 403 sheet: 0.37 (0.43), residues: 155 loop : -0.75 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 105 HIS 0.002 0.001 HIS R 296 PHE 0.014 0.001 PHE A 212 TYR 0.006 0.001 TYR B 111 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.741 Fit side-chains REVERT: G 38 MET cc_start: 0.7828 (tpp) cc_final: 0.7476 (mtp) REVERT: R 79 ASP cc_start: 0.8434 (t0) cc_final: 0.8224 (t0) REVERT: R 231 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8251 (tm-30) outliers start: 2 outliers final: 2 residues processed: 99 average time/residue: 0.1880 time to fit residues: 24.8895 Evaluate side-chains 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.0040 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105629 restraints weight = 33236.549| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 4.57 r_work: 0.3105 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6831 Z= 0.137 Angle : 0.445 8.324 9348 Z= 0.232 Chirality : 0.039 0.140 1119 Planarity : 0.003 0.036 1172 Dihedral : 6.864 145.029 1005 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.82 % Allowed : 12.97 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 902 helix: 2.84 (0.27), residues: 405 sheet: 0.30 (0.43), residues: 160 loop : -0.67 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 105 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.706 Fit side-chains REVERT: G 38 MET cc_start: 0.8558 (tpp) cc_final: 0.8230 (mtp) REVERT: R 79 ASP cc_start: 0.8700 (t0) cc_final: 0.8442 (t0) REVERT: R 82 MET cc_start: 0.7123 (tmm) cc_final: 0.6346 (ttp) REVERT: R 231 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8339 (tm-30) outliers start: 5 outliers final: 5 residues processed: 92 average time/residue: 0.1941 time to fit residues: 23.7819 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102820 restraints weight = 31758.910| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.29 r_work: 0.3100 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6831 Z= 0.154 Angle : 0.456 7.744 9348 Z= 0.240 Chirality : 0.039 0.143 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.925 143.670 1005 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.82 % Allowed : 13.63 % Favored : 85.55 % 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: 1.67 (0.29), residues: 902 helix: 2.79 (0.27), residues: 411 sheet: 0.18 (0.41), residues: 167 loop : -0.61 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.822 Fit side-chains REVERT: G 38 MET cc_start: 0.8583 (tpp) cc_final: 0.8223 (mtp) REVERT: R 79 ASP cc_start: 0.8677 (t0) cc_final: 0.8469 (t0) REVERT: R 82 MET cc_start: 0.7281 (tmm) cc_final: 0.6464 (ttp) REVERT: R 231 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.2097 time to fit residues: 26.2284 Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104201 restraints weight = 40247.882| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.86 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6831 Z= 0.125 Angle : 0.444 7.572 9348 Z= 0.233 Chirality : 0.039 0.138 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.867 143.819 1005 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.66 % Allowed : 13.79 % Favored : 85.55 % 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: 1.66 (0.29), residues: 902 helix: 2.87 (0.27), residues: 405 sheet: 0.17 (0.41), residues: 167 loop : -0.69 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.764 Fit side-chains REVERT: G 38 MET cc_start: 0.7831 (tpp) cc_final: 0.7446 (mtp) outliers start: 4 outliers final: 4 residues processed: 90 average time/residue: 0.2045 time to fit residues: 24.2416 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 40 optimal weight: 0.0170 chunk 87 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105873 restraints weight = 42629.652| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 5.25 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6831 Z= 0.110 Angle : 0.436 7.249 9348 Z= 0.228 Chirality : 0.038 0.136 1119 Planarity : 0.003 0.035 1172 Dihedral : 6.795 144.314 1005 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.66 % Allowed : 13.79 % Favored : 85.55 % 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: 1.71 (0.29), residues: 902 helix: 2.92 (0.27), residues: 404 sheet: 0.25 (0.42), residues: 165 loop : -0.69 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 313 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.57 seconds wall clock time: 62 minutes 22.53 seconds (3742.53 seconds total)