Starting phenix.real_space_refine on Sat May 10 16:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unv_42418/05_2025/8unv_42418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unv_42418/05_2025/8unv_42418.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/8unv_42418/05_2025/8unv_42418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unv_42418/05_2025/8unv_42418.map" model { file = "/net/cci-nas-00/data/ceres_data/8unv_42418/05_2025/8unv_42418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unv_42418/05_2025/8unv_42418.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= 0.023 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 4229 2.51 5 N 1136 2.21 5 O 1183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 6591 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1712 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 156 Conformer: "B" Number of residues, atoms: 233, 1712 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 156 bond proxies already assigned to first conformer: 1733 Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2383 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 164 Chain: "G" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 334 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2103 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} 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: 5.40, per 1000 atoms: 0.82 Number of scatterers: 6591 At special positions: 0 Unit cell: (84.1669, 137.097, 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 1183 8.00 N 1136 7.00 C 4229 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: 1.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 48.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.604A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.878A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.723A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.676A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.918A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.538A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.509A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.650A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 4.123A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.531A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.524A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.568A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 67 No H-bonds generated for 'chain 'R' and resid 66 through 67' Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.033A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.380A 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: 4.070A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.703A 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 171 removed outlier: 3.785A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.589A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.604A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.837A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.838A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.561A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.260A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.551A 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: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.085A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.598A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.092A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.733A 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: 6.920A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.520A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.836A 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: 3.883A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1020 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: 1.78 Time building geometry restraints manager: 1.99 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: 1485 1.33 - 1.45: 1511 1.45 - 1.57: 3681 1.57 - 1.69: 5 1.69 - 1.81: 54 Bond restraints: 6736 Sorted by residual: bond pdb=" C VAL R 31 " pdb=" O VAL R 31 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.17e-02 7.31e+03 2.43e+01 bond pdb=" C GLY R 35 " pdb=" O GLY R 35 " ideal model delta sigma weight residual 1.234 1.279 -0.045 1.20e-02 6.94e+03 1.43e+01 bond pdb=" C ILE R 154 " pdb=" N LEU R 155 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.36e-02 5.41e+03 1.42e+01 bond pdb=" N VAL R 31 " pdb=" CA VAL R 31 " ideal model delta sigma weight residual 1.461 1.504 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.461 1.502 -0.042 1.19e-02 7.06e+03 1.24e+01 ... (remaining 6731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 8927 2.36 - 4.73: 265 4.73 - 7.09: 23 7.09 - 9.46: 7 9.46 - 11.82: 4 Bond angle restraints: 9226 Sorted by residual: angle pdb=" N TRP R 173 " pdb=" CA TRP R 173 " pdb=" C TRP R 173 " ideal model delta sigma weight residual 111.28 117.67 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" C ILE R 47 " pdb=" N VAL R 48 " pdb=" CA VAL R 48 " ideal model delta sigma weight residual 122.35 115.84 6.51 1.18e+00 7.18e-01 3.05e+01 angle pdb=" CA GLY A 49 " pdb=" C GLY A 49 " pdb=" O GLY A 49 " ideal model delta sigma weight residual 121.41 116.66 4.75 8.80e-01 1.29e+00 2.92e+01 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 105.55 5.73 1.09e+00 8.42e-01 2.76e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 ... (remaining 9221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.34: 3777 31.34 - 62.69: 97 62.69 - 94.03: 7 94.03 - 125.37: 1 125.37 - 156.71: 2 Dihedral angle restraints: 3884 sinusoidal: 1223 harmonic: 2661 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 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+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 -134.02 -156.71 1 2.00e+01 2.50e-03 4.60e+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 -40.98 145.58 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 3881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 802 0.050 - 0.100: 187 0.100 - 0.150: 86 0.150 - 0.200: 22 0.200 - 0.250: 8 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA HIS R 172 " pdb=" N HIS R 172 " pdb=" C HIS R 172 " pdb=" CB HIS R 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET R 171 " pdb=" N MET R 171 " pdb=" C MET R 171 " pdb=" CB MET R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1102 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 60 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C PRO G 60 " 0.047 2.00e-02 2.50e+03 pdb=" O PRO G 60 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE G 61 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 52 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C THR G 52 " -0.046 2.00e-02 2.50e+03 pdb=" O THR G 52 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO G 53 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO G 49 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.035 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 508 2.74 - 3.28: 6460 3.28 - 3.82: 10316 3.82 - 4.36: 11413 4.36 - 4.90: 20961 Nonbonded interactions: 49658 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.201 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.316 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.403 3.040 nonbonded pdb=" OG SER A 51 " pdb=" O1G GTP A 401 " model vdw 2.405 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.431 3.120 ... (remaining 49653 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: 1.930 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.170 Find NCS groups from input model: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.006 0.058 6738 Z= 0.408 Angle : 0.866 11.820 9230 Z= 0.597 Chirality : 0.058 0.250 1105 Planarity : 0.004 0.062 1159 Dihedral : 14.497 156.713 2152 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.34 % Allowed : 1.69 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 900 helix: 1.84 (0.27), residues: 384 sheet: 0.53 (0.44), residues: 168 loop : -0.75 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.005 0.001 HIS R 178 PHE 0.021 0.001 PHE A 212 TYR 0.016 0.001 TYR R 174 ARG 0.002 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.19839 ( 349) hydrogen bonds : angle 7.14213 ( 1020) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.48848 ( 4) covalent geometry : bond 0.00566 ( 6736) covalent geometry : angle 0.86617 ( 9226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.812 Fit side-chains REVERT: A 211 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8213 (mtpt) REVERT: A 368 ASP cc_start: 0.7935 (t0) cc_final: 0.7299 (p0) REVERT: R 107 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7538 (mt-10) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.2005 time to fit residues: 27.5212 Evaluate side-chains 84 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095877 restraints weight = 38488.147| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 5.20 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6738 Z= 0.154 Angle : 0.521 6.704 9230 Z= 0.283 Chirality : 0.043 0.136 1105 Planarity : 0.004 0.049 1159 Dihedral : 8.173 131.222 1000 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 10.00 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 900 helix: 1.91 (0.26), residues: 399 sheet: 0.42 (0.43), residues: 178 loop : -0.87 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS R 178 PHE 0.013 0.001 PHE B 235 TYR 0.012 0.001 TYR R 174 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 349) hydrogen bonds : angle 4.65395 ( 1020) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.53306 ( 4) covalent geometry : bond 0.00350 ( 6736) covalent geometry : angle 0.52076 ( 9226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.680 Fit side-chains REVERT: A 211 LYS cc_start: 0.8545 (mtmm) cc_final: 0.7901 (mtpt) REVERT: A 368 ASP cc_start: 0.7570 (t0) cc_final: 0.7315 (t0) REVERT: R 318 ASN cc_start: 0.9077 (t0) cc_final: 0.8793 (t0) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.1924 time to fit residues: 24.2682 Evaluate side-chains 89 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096446 restraints weight = 33363.360| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 5.11 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6738 Z= 0.116 Angle : 0.479 6.999 9230 Z= 0.256 Chirality : 0.041 0.137 1105 Planarity : 0.003 0.042 1159 Dihedral : 7.404 123.004 998 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.02 % Allowed : 12.03 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 900 helix: 2.15 (0.26), residues: 402 sheet: 0.51 (0.42), residues: 176 loop : -0.87 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS R 178 PHE 0.008 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 349) hydrogen bonds : angle 4.20506 ( 1020) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.58323 ( 4) covalent geometry : bond 0.00252 ( 6736) covalent geometry : angle 0.47877 ( 9226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.683 Fit side-chains REVERT: A 211 LYS cc_start: 0.8518 (mtmm) cc_final: 0.7760 (mtpt) REVERT: A 368 ASP cc_start: 0.7701 (t0) cc_final: 0.7412 (t0) REVERT: G 48 ASP cc_start: 0.7496 (p0) cc_final: 0.7188 (p0) REVERT: R 174 TYR cc_start: 0.8088 (p90) cc_final: 0.7847 (p90) REVERT: R 318 ASN cc_start: 0.8963 (t0) cc_final: 0.8555 (t0) outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.1854 time to fit residues: 22.2015 Evaluate side-chains 85 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.127537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097541 restraints weight = 41832.323| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 5.54 r_work: 0.3035 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 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 = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6738 Z= 0.095 Angle : 0.454 6.957 9230 Z= 0.240 Chirality : 0.040 0.134 1105 Planarity : 0.003 0.038 1159 Dihedral : 6.900 116.936 998 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.36 % Allowed : 12.88 % Favored : 85.76 % 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: 900 helix: 2.36 (0.26), residues: 402 sheet: 0.37 (0.42), residues: 178 loop : -0.84 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.008 0.001 TYR R 174 ARG 0.001 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 349) hydrogen bonds : angle 3.92477 ( 1020) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.69399 ( 4) covalent geometry : bond 0.00196 ( 6736) covalent geometry : angle 0.45360 ( 9226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.772 Fit side-chains REVERT: A 211 LYS cc_start: 0.8542 (mtmm) cc_final: 0.7809 (mtpt) REVERT: A 344 GLU cc_start: 0.8885 (tp30) cc_final: 0.8567 (tp30) REVERT: A 368 ASP cc_start: 0.7818 (t0) cc_final: 0.7567 (t0) REVERT: B 234 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: G 48 ASP cc_start: 0.7663 (p0) cc_final: 0.7404 (p0) REVERT: R 174 TYR cc_start: 0.8230 (p90) cc_final: 0.7987 (p90) REVERT: R 318 ASN cc_start: 0.9000 (t0) cc_final: 0.8615 (t0) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1875 time to fit residues: 24.0522 Evaluate side-chains 91 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 chunk 62 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.093165 restraints weight = 29030.752| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.74 r_work: 0.2982 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6738 Z= 0.196 Angle : 0.532 6.564 9230 Z= 0.287 Chirality : 0.043 0.138 1105 Planarity : 0.003 0.041 1159 Dihedral : 6.589 105.590 998 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.53 % Allowed : 15.25 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 900 helix: 2.06 (0.26), residues: 400 sheet: 0.27 (0.42), residues: 179 loop : -1.04 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.005 0.001 HIS R 178 PHE 0.017 0.001 PHE B 235 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.05266 ( 349) hydrogen bonds : angle 4.29041 ( 1020) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.60773 ( 4) covalent geometry : bond 0.00469 ( 6736) covalent geometry : angle 0.53160 ( 9226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.712 Fit side-chains REVERT: A 211 LYS cc_start: 0.8670 (mtmm) cc_final: 0.7918 (mtpt) REVERT: A 368 ASP cc_start: 0.7929 (t0) cc_final: 0.7626 (t0) REVERT: B 234 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: R 318 ASN cc_start: 0.8974 (t0) cc_final: 0.8664 (t0) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.1988 time to fit residues: 23.2021 Evaluate side-chains 85 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 164 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 20 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3414 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.126948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097684 restraints weight = 36986.869| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 5.22 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6738 Z= 0.091 Angle : 0.449 6.465 9230 Z= 0.240 Chirality : 0.040 0.141 1105 Planarity : 0.003 0.040 1159 Dihedral : 5.934 96.117 998 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.02 % Allowed : 15.42 % Favored : 83.56 % 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: 1.29 (0.29), residues: 900 helix: 2.41 (0.26), residues: 402 sheet: 0.41 (0.43), residues: 170 loop : -0.90 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.004 0.001 HIS R 93 PHE 0.010 0.001 PHE R 217 TYR 0.015 0.001 TYR R 174 ARG 0.001 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 349) hydrogen bonds : angle 3.85619 ( 1020) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.70622 ( 4) covalent geometry : bond 0.00181 ( 6736) covalent geometry : angle 0.44873 ( 9226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.707 Fit side-chains REVERT: A 211 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7704 (mtpt) REVERT: A 368 ASP cc_start: 0.7925 (t0) cc_final: 0.7578 (t0) REVERT: B 234 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: R 318 ASN cc_start: 0.9012 (t0) cc_final: 0.8541 (t0) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.1965 time to fit residues: 22.8243 Evaluate side-chains 85 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 45 optimal weight: 0.0370 overall best weight: 0.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102140 restraints weight = 42866.360| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 5.48 r_work: 0.3104 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 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 = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6738 Z= 0.085 Angle : 0.449 7.772 9230 Z= 0.237 Chirality : 0.040 0.137 1105 Planarity : 0.003 0.048 1159 Dihedral : 5.380 87.525 998 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 15.42 % Favored : 83.05 % 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: 1.54 (0.29), residues: 900 helix: 2.77 (0.27), residues: 390 sheet: 0.44 (0.42), residues: 171 loop : -0.80 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.004 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.019 0.001 TYR R 174 ARG 0.001 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 349) hydrogen bonds : angle 3.67498 ( 1020) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.80369 ( 4) covalent geometry : bond 0.00162 ( 6736) covalent geometry : angle 0.44835 ( 9226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.831 Fit side-chains REVERT: A 211 LYS cc_start: 0.8605 (mtmm) cc_final: 0.7951 (mtpt) REVERT: B 234 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8763 (m-80) REVERT: R 318 ASN cc_start: 0.9272 (t0) cc_final: 0.8867 (t0) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 0.2112 time to fit residues: 26.6206 Evaluate side-chains 90 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 174 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 371 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093529 restraints weight = 41656.521| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.43 r_work: 0.2972 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6738 Z= 0.179 Angle : 0.520 6.682 9230 Z= 0.279 Chirality : 0.042 0.134 1105 Planarity : 0.004 0.058 1159 Dihedral : 5.627 89.402 998 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.68 % Favored : 97.21 % Rotamer: Outliers : 1.69 % Allowed : 16.78 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 900 helix: 2.42 (0.26), residues: 402 sheet: 0.37 (0.42), residues: 174 loop : -1.01 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.014 0.001 PHE B 235 TYR 0.019 0.001 TYR R 174 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 349) hydrogen bonds : angle 4.03541 ( 1020) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.62726 ( 4) covalent geometry : bond 0.00427 ( 6736) covalent geometry : angle 0.52005 ( 9226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.954 Fit side-chains REVERT: A 211 LYS cc_start: 0.8688 (mtmm) cc_final: 0.7944 (mtpt) REVERT: B 234 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8685 (m-80) REVERT: R 318 ASN cc_start: 0.9000 (t0) cc_final: 0.8692 (t0) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.2137 time to fit residues: 23.6812 Evaluate side-chains 86 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096958 restraints weight = 31408.388| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.83 r_work: 0.3033 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6738 Z= 0.107 Angle : 0.473 6.550 9230 Z= 0.252 Chirality : 0.041 0.130 1105 Planarity : 0.003 0.062 1159 Dihedral : 5.383 86.566 998 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.53 % Allowed : 16.95 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 900 helix: 2.52 (0.26), residues: 402 sheet: 0.32 (0.42), residues: 171 loop : -0.96 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE R 217 TYR 0.017 0.001 TYR R 174 ARG 0.001 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 349) hydrogen bonds : angle 3.84666 ( 1020) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.65155 ( 4) covalent geometry : bond 0.00234 ( 6736) covalent geometry : angle 0.47275 ( 9226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.698 Fit side-chains REVERT: A 211 LYS cc_start: 0.8572 (mtmm) cc_final: 0.7826 (mtpt) REVERT: B 234 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: R 318 ASN cc_start: 0.9030 (t0) cc_final: 0.8726 (t0) outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.1942 time to fit residues: 21.9086 Evaluate side-chains 84 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097774 restraints weight = 34590.177| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 5.07 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6738 Z= 0.094 Angle : 0.467 6.974 9230 Z= 0.247 Chirality : 0.040 0.134 1105 Planarity : 0.003 0.065 1159 Dihedral : 5.140 83.356 998 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.66 % Rotamer: Outliers : 1.19 % Allowed : 17.46 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 900 helix: 2.57 (0.26), residues: 402 sheet: 0.34 (0.42), residues: 171 loop : -0.94 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 173 HIS 0.004 0.001 HIS R 93 PHE 0.007 0.001 PHE A 212 TYR 0.019 0.001 TYR R 174 ARG 0.001 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 349) hydrogen bonds : angle 3.75350 ( 1020) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.68738 ( 4) covalent geometry : bond 0.00198 ( 6736) covalent geometry : angle 0.46644 ( 9226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.768 Fit side-chains REVERT: A 211 LYS cc_start: 0.8482 (mtmm) cc_final: 0.7720 (mtpt) REVERT: B 234 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: R 171 MET cc_start: 0.7451 (ptp) cc_final: 0.7240 (ptt) REVERT: R 318 ASN cc_start: 0.9049 (t0) cc_final: 0.8727 (t0) outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 0.2026 time to fit residues: 23.7838 Evaluate side-chains 91 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.0470 chunk 76 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099420 restraints weight = 40779.983| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 5.34 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6738 Z= 0.094 Angle : 0.463 6.724 9230 Z= 0.245 Chirality : 0.040 0.132 1105 Planarity : 0.003 0.064 1159 Dihedral : 5.019 81.359 998 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.53 % Allowed : 17.12 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 900 helix: 2.74 (0.26), residues: 390 sheet: 0.28 (0.42), residues: 173 loop : -0.90 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.007 0.001 PHE A 212 TYR 0.020 0.001 TYR R 174 ARG 0.001 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 349) hydrogen bonds : angle 3.71420 ( 1020) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.69256 ( 4) covalent geometry : bond 0.00197 ( 6736) covalent geometry : angle 0.46331 ( 9226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.40 seconds wall clock time: 61 minutes 11.58 seconds (3671.58 seconds total)