Starting phenix.real_space_refine on Sat May 10 18:49:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unq_42413/05_2025/8unq_42413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unq_42413/05_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_42413/05_2025/8unq_42413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unq_42413/05_2025/8unq_42413.map" model { file = "/net/cci-nas-00/data/ceres_data/8unq_42413/05_2025/8unq_42413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unq_42413/05_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-5687/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: 5.33, per 1000 atoms: 0.80 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 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: 0.79 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: 1.76 Time building geometry restraints manager: 1.90 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: 1.570 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.830 Find NCS groups from input model: 0.070 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- 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 6833 Z= 0.303 Angle : 0.766 11.509 9352 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 Details of bonding type rmsd hydrogen bonds : bond 0.20167 ( 356) hydrogen bonds : angle 6.78438 ( 1032) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.91142 ( 4) covalent geometry : bond 0.00445 ( 6831) covalent geometry : angle 0.76578 ( 9348) *********************** 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 : 0.669 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: 0.1931 time to fit residues: 28.0642 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 : 0.673 ------------------------------------------------------------------------------- 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 = 0.100836 restraints weight = 30055.204| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.33 r_work: 0.3129 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 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 = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 6833 Z= 0.164 Angle : 0.532 6.977 9352 Z= 0.286 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 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 356) hydrogen bonds : angle 4.76964 ( 1032) SS BOND : bond 0.00370 ( 2) SS BOND : angle 2.63148 ( 4) covalent geometry : bond 0.00379 ( 6831) covalent geometry : angle 0.52975 ( 9348) *********************** 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 : 0.689 Fit side-chains REVERT: G 38 MET cc_start: 0.8580 (tpp) cc_final: 0.8231 (mtp) outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.1909 time to fit residues: 23.1401 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 : 0.681 ------------------------------------------------------------------------------- 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: 0.0670 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.125711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100422 restraints weight = 24890.831| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.86 r_work: 0.3142 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 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 = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6833 Z= 0.181 Angle : 0.523 6.284 9352 Z= 0.283 Chirality : 0.042 0.158 1119 Planarity : 0.003 0.041 1172 Dihedral : 7.412 142.737 1005 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.99 % Allowed : 11.49 % Favored : 87.52 % 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: 2.22 (0.27), residues: 412 sheet: -0.05 (0.41), residues: 162 loop : -0.81 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE B 241 TYR 0.014 0.001 TYR R 308 ARG 0.002 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05366 ( 356) hydrogen bonds : angle 4.51520 ( 1032) SS BOND : bond 0.00038 ( 2) SS BOND : angle 2.41199 ( 4) covalent geometry : bond 0.00433 ( 6831) covalent geometry : angle 0.52045 ( 9348) *********************** 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 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.777 Fit side-chains REVERT: G 38 MET cc_start: 0.8482 (tpp) cc_final: 0.8111 (mtp) outliers start: 6 outliers final: 5 residues processed: 92 average time/residue: 0.2085 time to fit residues: 25.2012 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 157 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102436 restraints weight = 28716.099| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.45 r_work: 0.3146 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6833 Z= 0.123 Angle : 0.463 6.297 9352 Z= 0.251 Chirality : 0.040 0.145 1119 Planarity : 0.003 0.040 1172 Dihedral : 7.171 143.168 1005 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.82 % Allowed : 12.81 % Favored : 86.37 % 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: 1.17 (0.29), residues: 902 helix: 2.38 (0.27), residues: 410 sheet: -0.11 (0.41), residues: 162 loop : -0.83 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.008 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 356) hydrogen bonds : angle 4.21907 ( 1032) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.54161 ( 4) covalent geometry : bond 0.00278 ( 6831) covalent geometry : angle 0.46224 ( 9348) *********************** 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 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.745 Fit side-chains REVERT: B 59 TYR cc_start: 0.8659 (m-80) cc_final: 0.7005 (m-80) REVERT: G 38 MET cc_start: 0.8495 (tpp) cc_final: 0.8120 (mtp) outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.2060 time to fit residues: 26.0512 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.124155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099755 restraints weight = 41479.577| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.48 r_work: 0.3024 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6833 Z= 0.146 Angle : 0.486 6.361 9352 Z= 0.263 Chirality : 0.041 0.151 1119 Planarity : 0.003 0.041 1172 Dihedral : 7.202 142.328 1005 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.99 % Allowed : 13.14 % Favored : 85.88 % 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: 1.11 (0.29), residues: 902 helix: 2.38 (0.27), residues: 410 sheet: -0.21 (0.40), residues: 162 loop : -0.89 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.007 0.001 HIS A 220 PHE 0.015 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 356) hydrogen bonds : angle 4.23395 ( 1032) SS BOND : bond 0.00141 ( 2) SS BOND : angle 2.22886 ( 4) covalent geometry : bond 0.00344 ( 6831) covalent geometry : angle 0.48356 ( 9348) *********************** 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 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.766 Fit side-chains REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7715 (t80) REVERT: G 38 MET cc_start: 0.8573 (tpp) cc_final: 0.8200 (mtp) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.2045 time to fit residues: 23.8274 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.126110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100841 restraints weight = 36515.285| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.86 r_work: 0.3040 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6833 Z= 0.111 Angle : 0.451 6.318 9352 Z= 0.244 Chirality : 0.040 0.143 1119 Planarity : 0.003 0.039 1172 Dihedral : 7.118 142.663 1005 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.15 % Allowed : 13.46 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 902 helix: 2.47 (0.27), residues: 410 sheet: -0.13 (0.41), residues: 162 loop : -0.84 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.002 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 356) hydrogen bonds : angle 4.07285 ( 1032) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.97150 ( 4) covalent geometry : bond 0.00246 ( 6831) covalent geometry : angle 0.44953 ( 9348) *********************** 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 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.800 Fit side-chains REVERT: B 234 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7584 (t80) REVERT: G 38 MET cc_start: 0.8535 (tpp) cc_final: 0.8154 (mtp) REVERT: R 231 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.2018 time to fit residues: 24.2134 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.127106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101572 restraints weight = 39513.676| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.12 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6833 Z= 0.100 Angle : 0.446 7.145 9352 Z= 0.238 Chirality : 0.039 0.142 1119 Planarity : 0.003 0.039 1172 Dihedral : 7.045 143.095 1005 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.82 % Allowed : 14.45 % Favored : 84.73 % 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: 1.33 (0.29), residues: 902 helix: 2.55 (0.27), residues: 410 sheet: -0.06 (0.42), residues: 162 loop : -0.80 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 63 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 356) hydrogen bonds : angle 3.97131 ( 1032) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.68423 ( 4) covalent geometry : bond 0.00215 ( 6831) covalent geometry : angle 0.44440 ( 9348) *********************** 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 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.687 Fit side-chains REVERT: A 295 ASP cc_start: 0.8486 (p0) cc_final: 0.8276 (p0) REVERT: B 234 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7436 (t80) REVERT: G 38 MET cc_start: 0.7734 (tpp) cc_final: 0.7322 (mtp) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.2062 time to fit residues: 24.2933 Evaluate side-chains 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.0470 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.127488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103105 restraints weight = 33102.767| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.30 r_work: 0.3086 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 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 = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6833 Z= 0.090 Angle : 0.437 6.329 9352 Z= 0.233 Chirality : 0.039 0.139 1119 Planarity : 0.003 0.038 1172 Dihedral : 6.958 143.622 1005 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.82 % Allowed : 14.61 % Favored : 84.56 % 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: 1.47 (0.29), residues: 902 helix: 2.65 (0.27), residues: 410 sheet: 0.13 (0.42), residues: 160 loop : -0.76 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 105 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 356) hydrogen bonds : angle 3.87370 ( 1032) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.48758 ( 4) covalent geometry : bond 0.00185 ( 6831) covalent geometry : angle 0.43642 ( 9348) *********************** 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 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.811 Fit side-chains REVERT: B 234 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7361 (t80) REVERT: G 38 MET cc_start: 0.8501 (tpp) cc_final: 0.8145 (mtp) REVERT: R 231 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8379 (tm-30) outliers start: 5 outliers final: 4 residues processed: 91 average time/residue: 0.2035 time to fit residues: 24.6854 Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 314 ILE 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: 0.5980 chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.126990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102661 restraints weight = 31770.674| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.21 r_work: 0.3083 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 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 = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6833 Z= 0.097 Angle : 0.452 8.876 9352 Z= 0.237 Chirality : 0.039 0.142 1119 Planarity : 0.003 0.038 1172 Dihedral : 6.974 143.468 1005 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.82 % Allowed : 14.78 % Favored : 84.40 % 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: 1.52 (0.29), residues: 902 helix: 2.71 (0.27), residues: 410 sheet: 0.14 (0.42), residues: 160 loop : -0.75 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 105 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 356) hydrogen bonds : angle 3.87493 ( 1032) SS BOND : bond 0.00141 ( 2) SS BOND : angle 1.47138 ( 4) covalent geometry : bond 0.00211 ( 6831) covalent geometry : angle 0.45073 ( 9348) *********************** 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 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.626 Fit side-chains REVERT: B 234 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7416 (t80) REVERT: G 38 MET cc_start: 0.8501 (tpp) cc_final: 0.8139 (mtp) REVERT: R 79 ASP cc_start: 0.8659 (t0) cc_final: 0.8450 (t0) REVERT: R 231 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8351 (tm-30) outliers start: 5 outliers final: 4 residues processed: 88 average time/residue: 0.2111 time to fit residues: 24.5350 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.126968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102304 restraints weight = 40389.369| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.72 r_work: 0.3065 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6833 Z= 0.099 Angle : 0.451 7.938 9352 Z= 0.237 Chirality : 0.039 0.141 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.967 143.249 1005 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.99 % Allowed : 14.94 % Favored : 84.07 % 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: 1.52 (0.29), residues: 902 helix: 2.73 (0.27), residues: 410 sheet: 0.10 (0.42), residues: 160 loop : -0.76 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 105 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.010 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 356) hydrogen bonds : angle 3.86348 ( 1032) SS BOND : bond 0.00159 ( 2) SS BOND : angle 1.46998 ( 4) covalent geometry : bond 0.00215 ( 6831) covalent geometry : angle 0.44957 ( 9348) ********************** 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 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.704 Fit side-chains REVERT: B 234 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7401 (t80) REVERT: G 38 MET cc_start: 0.8532 (tpp) cc_final: 0.8171 (mtp) REVERT: R 231 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8362 (tm-30) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.2100 time to fit residues: 24.4760 Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE 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 314 ILE 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: 2.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.127405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103012 restraints weight = 42748.729| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 5.10 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6833 Z= 0.097 Angle : 0.450 8.047 9352 Z= 0.236 Chirality : 0.039 0.141 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.947 143.097 1005 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.82 % Allowed : 15.11 % Favored : 84.07 % 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: 1.55 (0.29), residues: 902 helix: 2.74 (0.27), residues: 410 sheet: 0.07 (0.41), residues: 167 loop : -0.72 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 105 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 356) hydrogen bonds : angle 3.84255 ( 1032) SS BOND : bond 0.00141 ( 2) SS BOND : angle 1.45924 ( 4) covalent geometry : bond 0.00210 ( 6831) covalent geometry : angle 0.44870 ( 9348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3590.56 seconds wall clock time: 62 minutes 50.91 seconds (3770.91 seconds total)