Starting phenix.real_space_refine on Wed Mar 12 00:09:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ddf_7869/03_2025/6ddf_7869_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ddf_7869/03_2025/6ddf_7869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ddf_7869/03_2025/6ddf_7869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ddf_7869/03_2025/6ddf_7869.map" model { file = "/net/cci-nas-00/data/ceres_data/6ddf_7869/03_2025/6ddf_7869_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ddf_7869/03_2025/6ddf_7869_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.567 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4342 2.51 5 N 1165 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6808 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1694 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 396 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2134 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.22, per 1000 atoms: 0.62 Number of scatterers: 6808 At special positions: 0 Unit cell: (76.96, 118.56, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1249 8.00 N 1165 7.00 C 4342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " 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=1, symmetry=0 Links applied TRANS " DAL D 2 " - " TYR D 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 938.2 milliseconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 2 " Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 4.094A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.560A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.545A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 5.163A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.834A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.720A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.601A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 4.323A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 removed outlier: 3.672A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 97 removed outlier: 3.768A pdb=" N LEU R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS R 79 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.999A pdb=" N ILE R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 130 removed outlier: 3.627A pdb=" N SER R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN R 127 " --> pdb=" O PHE R 123 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR R 128 " --> pdb=" O GLN R 124 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 171 removed outlier: 3.795A pdb=" N CYS R 140 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 Processing helix chain 'R' and resid 182 through 204 removed outlier: 3.612A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 229 through 241 removed outlier: 3.956A pdb=" N LYS R 233 " --> pdb=" O GLU R 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 249 Processing helix chain 'R' and resid 249 through 260 removed outlier: 4.254A pdb=" N MET R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 294 Processing helix chain 'R' and resid 294 through 306 removed outlier: 3.826A pdb=" N VAL R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 305 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 326 removed outlier: 4.027A pdb=" N SER R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 336 Proline residue: R 333 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.911A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 6.664A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.594A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.617A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 79 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.613A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.895A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.629A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.436A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.671A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 849 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: 1.65 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: 1.20 - 1.33: 1369 1.33 - 1.45: 1720 1.45 - 1.58: 3779 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 6943 Sorted by residual: bond pdb=" C LEU B 79 " pdb=" O LEU B 79 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.24e-02 6.50e+03 7.30e+00 bond pdb=" O ETA D 5 " pdb=" CB ETA D 5 " ideal model delta sigma weight residual 1.413 1.459 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.35e-02 5.49e+03 4.34e+00 bond pdb=" CB PRO R 244 " pdb=" CG PRO R 244 " ideal model delta sigma weight residual 1.492 1.392 0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 1.524 1.504 0.021 1.22e-02 6.72e+03 2.88e+00 ... (remaining 6938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9027 2.19 - 4.39: 331 4.39 - 6.58: 46 6.58 - 8.77: 15 8.77 - 10.97: 8 Bond angle restraints: 9427 Sorted by residual: angle pdb=" N LEU R 121 " pdb=" CA LEU R 121 " pdb=" C LEU R 121 " ideal model delta sigma weight residual 109.81 120.78 -10.97 2.21e+00 2.05e-01 2.46e+01 angle pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N MEA D 4 " pdb=" CA MEA D 4 " pdb=" CB MEA D 4 " ideal model delta sigma weight residual 110.50 117.47 -6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C ASP B 27 " pdb=" N ALA B 28 " pdb=" CA ALA B 28 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" N LEU B 79 " pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 108.96 103.24 5.72 1.59e+00 3.96e-01 1.29e+01 ... (remaining 9422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.19: 3677 12.19 - 24.39: 324 24.39 - 36.58: 74 36.58 - 48.78: 27 48.78 - 60.97: 1 Dihedral angle restraints: 4103 sinusoidal: 1503 harmonic: 2600 Sorted by residual: dihedral pdb=" CA ILE A 49 " pdb=" C ILE A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA SER R 214 " pdb=" C SER R 214 " pdb=" N ILE R 215 " pdb=" CA ILE R 215 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 151.90 28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 4100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 796 0.057 - 0.113: 251 0.113 - 0.170: 41 0.170 - 0.227: 7 0.227 - 0.284: 3 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA LEU R 121 " pdb=" N LEU R 121 " pdb=" C LEU R 121 " pdb=" CB LEU R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B 37 " pdb=" CA ILE B 37 " pdb=" CG1 ILE B 37 " pdb=" CG2 ILE B 37 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1095 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.014 2.00e-02 2.50e+03 1.66e-02 6.88e+00 pdb=" CG TRP B 63 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 49 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 180 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO R 181 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " -0.032 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1188 2.76 - 3.30: 6364 3.30 - 3.83: 11292 3.83 - 4.37: 12756 4.37 - 4.90: 22133 Nonbonded interactions: 53733 Sorted by model distance: nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 246 " model vdw 2.228 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.310 3.040 nonbonded pdb=" N THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.313 3.120 ... (remaining 53728 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 0.100 6943 Z= 0.399 Angle : 1.014 10.968 9427 Z= 0.540 Chirality : 0.057 0.284 1098 Planarity : 0.007 0.065 1189 Dihedral : 10.482 60.972 2411 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.34 % Favored : 91.54 % Rotamer: Outliers : 0.72 % Allowed : 5.15 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.62 (0.23), residues: 875 helix: -2.94 (0.19), residues: 347 sheet: -3.53 (0.36), residues: 159 loop : -2.74 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 63 HIS 0.011 0.002 HIS B 183 PHE 0.031 0.003 PHE B 241 TYR 0.031 0.003 TYR R 299 ARG 0.004 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 246 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7114 (t70) cc_final: 0.6641 (t0) REVERT: B 65 THR cc_start: 0.7469 (p) cc_final: 0.7212 (p) REVERT: B 78 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7742 (mmtt) REVERT: B 123 ILE cc_start: 0.8588 (pp) cc_final: 0.8376 (pt) REVERT: R 162 SER cc_start: 0.8137 (t) cc_final: 0.7889 (t) REVERT: R 198 ILE cc_start: 0.3926 (tp) cc_final: 0.3041 (mt) REVERT: R 216 ASP cc_start: 0.7316 (t0) cc_final: 0.6711 (t0) REVERT: R 336 TYR cc_start: 0.7601 (m-10) cc_final: 0.7219 (m-80) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.2184 time to fit residues: 69.0054 Evaluate side-chains 161 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 244 HIS A 269 ASN A 294 ASN B 13 GLN B 88 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125017 restraints weight = 11762.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129037 restraints weight = 6505.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131839 restraints weight = 4200.084| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6943 Z= 0.202 Angle : 0.673 9.027 9427 Z= 0.345 Chirality : 0.042 0.135 1098 Planarity : 0.005 0.044 1189 Dihedral : 6.057 64.944 959 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.72 % Allowed : 15.31 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.22 (0.26), residues: 875 helix: -1.12 (0.25), residues: 341 sheet: -3.17 (0.36), residues: 161 loop : -2.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE B 151 TYR 0.015 0.001 TYR R 149 ARG 0.006 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8879 (t70) cc_final: 0.8240 (t0) REVERT: B 215 GLU cc_start: 0.7694 (pm20) cc_final: 0.7140 (pm20) REVERT: B 219 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7715 (mmt90) REVERT: B 222 PHE cc_start: 0.8508 (m-10) cc_final: 0.8158 (m-10) REVERT: B 230 ASN cc_start: 0.8804 (t0) cc_final: 0.8320 (m110) REVERT: B 234 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: B 339 TRP cc_start: 0.8871 (m100) cc_final: 0.8561 (m-10) REVERT: C 32 LYS cc_start: 0.6960 (tppt) cc_final: 0.6049 (mttm) REVERT: R 239 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: R 248 ILE cc_start: 0.8186 (pt) cc_final: 0.7954 (mt) REVERT: R 292 CYS cc_start: 0.8429 (m) cc_final: 0.8185 (m) REVERT: R 324 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7067 (pt) outliers start: 26 outliers final: 17 residues processed: 214 average time/residue: 0.2035 time to fit residues: 56.1153 Evaluate side-chains 183 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 PHE Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130417 restraints weight = 11455.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134712 restraints weight = 6087.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137643 restraints weight = 3850.142| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6943 Z= 0.219 Angle : 0.657 8.950 9427 Z= 0.333 Chirality : 0.042 0.131 1098 Planarity : 0.004 0.037 1189 Dihedral : 5.663 60.342 959 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.15 % Allowed : 18.74 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.70 (0.28), residues: 875 helix: -0.50 (0.27), residues: 346 sheet: -3.05 (0.37), residues: 152 loop : -2.40 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE B 234 TYR 0.017 0.002 TYR R 149 ARG 0.006 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8774 (t70) cc_final: 0.7877 (t0) REVERT: B 78 LYS cc_start: 0.9004 (mmpt) cc_final: 0.8544 (mmtp) REVERT: B 117 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7712 (tt) REVERT: B 234 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8153 (m-10) REVERT: C 32 LYS cc_start: 0.7239 (tppt) cc_final: 0.6731 (mtmt) REVERT: R 293 TRP cc_start: 0.8299 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: R 314 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: R 324 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7253 (pt) outliers start: 36 outliers final: 18 residues processed: 188 average time/residue: 0.2107 time to fit residues: 50.9699 Evaluate side-chains 179 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 322 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 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 213 HIS B 13 GLN B 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117482 restraints weight = 11826.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121623 restraints weight = 6528.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124469 restraints weight = 4194.497| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6943 Z= 0.206 Angle : 0.637 9.153 9427 Z= 0.325 Chirality : 0.042 0.128 1098 Planarity : 0.004 0.035 1189 Dihedral : 5.503 61.661 959 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.86 % Allowed : 19.74 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.41 (0.28), residues: 875 helix: -0.30 (0.27), residues: 352 sheet: -2.94 (0.36), residues: 156 loop : -2.19 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.024 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.008 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8891 (t70) cc_final: 0.8268 (t0) REVERT: A 186 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 198 MET cc_start: 0.8229 (mmp) cc_final: 0.7804 (mmp) REVERT: A 313 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.7796 (ptm160) REVERT: B 75 GLN cc_start: 0.8561 (mm110) cc_final: 0.8020 (mm110) REVERT: B 117 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7548 (tt) REVERT: B 212 ASP cc_start: 0.7142 (p0) cc_final: 0.6415 (p0) REVERT: B 219 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7376 (mmt90) REVERT: B 234 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: B 275 SER cc_start: 0.8557 (t) cc_final: 0.8339 (t) REVERT: B 339 TRP cc_start: 0.8865 (m-10) cc_final: 0.8382 (m-10) REVERT: C 32 LYS cc_start: 0.6539 (tppt) cc_final: 0.6033 (mtmm) REVERT: R 83 LEU cc_start: 0.7842 (tm) cc_final: 0.7465 (tm) REVERT: R 179 ARG cc_start: 0.9074 (ptm-80) cc_final: 0.8652 (ptm160) REVERT: R 293 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.6854 (m-10) outliers start: 34 outliers final: 21 residues processed: 189 average time/residue: 0.1994 time to fit residues: 48.9955 Evaluate side-chains 178 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.0040 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122816 restraints weight = 11763.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126727 restraints weight = 6564.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129438 restraints weight = 4238.760| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6943 Z= 0.178 Angle : 0.623 10.977 9427 Z= 0.314 Chirality : 0.042 0.149 1098 Planarity : 0.004 0.034 1189 Dihedral : 5.353 64.914 959 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.01 % Allowed : 20.89 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.17 (0.29), residues: 875 helix: -0.11 (0.27), residues: 349 sheet: -2.66 (0.38), residues: 155 loop : -2.10 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.026 0.001 PHE B 222 TYR 0.019 0.001 TYR R 149 ARG 0.006 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8889 (t70) cc_final: 0.8046 (t0) REVERT: A 32 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7467 (ttm110) REVERT: A 186 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 310 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 313 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.7941 (ptm160) REVERT: B 78 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8535 (mmtp) REVERT: B 82 TRP cc_start: 0.8641 (m100) cc_final: 0.7436 (m100) REVERT: B 117 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7477 (tt) REVERT: B 164 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8576 (p) REVERT: B 188 MET cc_start: 0.8473 (tpp) cc_final: 0.7989 (tpp) REVERT: B 200 VAL cc_start: 0.9008 (m) cc_final: 0.8758 (m) REVERT: B 212 ASP cc_start: 0.6966 (p0) cc_final: 0.6090 (p0) REVERT: B 215 GLU cc_start: 0.7961 (pm20) cc_final: 0.7438 (pm20) REVERT: B 219 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7443 (mmt90) REVERT: B 234 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: B 275 SER cc_start: 0.8691 (t) cc_final: 0.8445 (t) REVERT: B 339 TRP cc_start: 0.8922 (m100) cc_final: 0.8541 (m-10) REVERT: C 32 LYS cc_start: 0.6548 (tppt) cc_final: 0.6041 (mtmm) REVERT: R 83 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7314 (tp) REVERT: R 87 PHE cc_start: 0.7868 (m-80) cc_final: 0.7582 (m-80) REVERT: R 179 ARG cc_start: 0.9072 (ptm-80) cc_final: 0.8724 (ptm160) REVERT: R 211 ARG cc_start: 0.5981 (mtt90) cc_final: 0.5711 (mtt90) REVERT: R 293 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.6772 (m-10) outliers start: 35 outliers final: 21 residues processed: 189 average time/residue: 0.2070 time to fit residues: 51.2362 Evaluate side-chains 183 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 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 269 ASN A 306 GLN B 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121264 restraints weight = 11869.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125156 restraints weight = 6633.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127870 restraints weight = 4320.346| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6943 Z= 0.195 Angle : 0.621 9.134 9427 Z= 0.314 Chirality : 0.042 0.147 1098 Planarity : 0.004 0.034 1189 Dihedral : 5.168 63.435 957 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.58 % Allowed : 22.75 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.88 (0.29), residues: 875 helix: 0.17 (0.28), residues: 349 sheet: -2.43 (0.39), residues: 156 loop : -2.05 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.026 0.001 PHE B 222 TYR 0.019 0.001 TYR R 149 ARG 0.005 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8902 (t70) cc_final: 0.8122 (t0) REVERT: A 186 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 198 MET cc_start: 0.8291 (mmp) cc_final: 0.7941 (mmp) REVERT: A 214 CYS cc_start: 0.8952 (t) cc_final: 0.8741 (m) REVERT: A 310 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 313 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.7902 (ptm160) REVERT: B 117 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 164 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8563 (p) REVERT: B 188 MET cc_start: 0.8522 (tpp) cc_final: 0.8060 (tpp) REVERT: B 200 VAL cc_start: 0.9058 (m) cc_final: 0.8681 (m) REVERT: B 212 ASP cc_start: 0.7080 (p0) cc_final: 0.6005 (p0) REVERT: B 215 GLU cc_start: 0.8044 (pm20) cc_final: 0.7559 (pm20) REVERT: B 219 ARG cc_start: 0.8043 (ttm170) cc_final: 0.7434 (mmt90) REVERT: B 234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: B 339 TRP cc_start: 0.9045 (m100) cc_final: 0.8602 (m-10) REVERT: C 32 LYS cc_start: 0.6486 (tppt) cc_final: 0.5958 (mtmm) REVERT: R 83 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7467 (tm) REVERT: R 87 PHE cc_start: 0.7803 (m-80) cc_final: 0.7545 (m-80) REVERT: R 179 ARG cc_start: 0.9074 (ptm-80) cc_final: 0.8724 (ptm160) REVERT: R 293 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.6604 (m-10) outliers start: 32 outliers final: 21 residues processed: 185 average time/residue: 0.2017 time to fit residues: 48.8049 Evaluate side-chains 177 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN R 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121904 restraints weight = 11709.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125938 restraints weight = 6420.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128729 restraints weight = 4092.843| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6943 Z= 0.189 Angle : 0.625 8.808 9427 Z= 0.315 Chirality : 0.042 0.151 1098 Planarity : 0.004 0.035 1189 Dihedral : 5.118 64.553 957 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.86 % Allowed : 22.75 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.29), residues: 875 helix: 0.37 (0.28), residues: 343 sheet: -2.25 (0.39), residues: 155 loop : -1.94 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.024 0.001 PHE B 222 TYR 0.018 0.001 TYR R 149 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8862 (t70) cc_final: 0.8160 (t0) REVERT: A 32 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7234 (ttm110) REVERT: A 186 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 214 CYS cc_start: 0.9058 (t) cc_final: 0.8729 (m) REVERT: A 247 MET cc_start: 0.7807 (mtm) cc_final: 0.7449 (mtt) REVERT: A 310 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7256 (tp) REVERT: A 313 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.7965 (ptm160) REVERT: B 117 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7704 (tt) REVERT: B 164 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8640 (p) REVERT: B 200 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8595 (m) REVERT: B 212 ASP cc_start: 0.7067 (p0) cc_final: 0.6079 (p0) REVERT: B 222 PHE cc_start: 0.8719 (m-10) cc_final: 0.8509 (m-80) REVERT: B 234 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: B 297 TRP cc_start: 0.8672 (m100) cc_final: 0.8433 (m100) REVERT: B 339 TRP cc_start: 0.9098 (m100) cc_final: 0.8642 (m-10) REVERT: C 11 GLN cc_start: 0.6652 (pm20) cc_final: 0.5964 (tm-30) REVERT: C 32 LYS cc_start: 0.6302 (tppt) cc_final: 0.5726 (mttt) REVERT: R 83 LEU cc_start: 0.7663 (tm) cc_final: 0.7441 (tm) REVERT: R 177 ASP cc_start: 0.8412 (t0) cc_final: 0.7939 (t0) REVERT: R 179 ARG cc_start: 0.9056 (ptm-80) cc_final: 0.8787 (ptm160) REVERT: R 241 PHE cc_start: 0.7239 (t80) cc_final: 0.6952 (t80) REVERT: R 251 CYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8150 (t) REVERT: R 255 MET cc_start: 0.8652 (ttt) cc_final: 0.8303 (ttt) REVERT: R 293 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.6527 (m-10) outliers start: 34 outliers final: 22 residues processed: 191 average time/residue: 0.1933 time to fit residues: 48.2543 Evaluate side-chains 188 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN C 18 GLN R 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117742 restraints weight = 11934.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121915 restraints weight = 6423.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124725 restraints weight = 4054.670| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6943 Z= 0.197 Angle : 0.637 10.042 9427 Z= 0.317 Chirality : 0.042 0.161 1098 Planarity : 0.004 0.034 1189 Dihedral : 5.080 64.808 957 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.29 % Allowed : 24.75 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.49 (0.30), residues: 875 helix: 0.48 (0.28), residues: 344 sheet: -2.12 (0.40), residues: 146 loop : -1.85 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.020 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8850 (t70) cc_final: 0.8141 (t0) REVERT: A 186 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 198 MET cc_start: 0.8110 (mmp) cc_final: 0.7841 (mmp) REVERT: A 214 CYS cc_start: 0.9055 (t) cc_final: 0.8680 (m) REVERT: A 247 MET cc_start: 0.7847 (mtm) cc_final: 0.7486 (mtt) REVERT: A 276 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5236 (tp30) REVERT: A 310 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7492 (tp) REVERT: A 313 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.7905 (ptm160) REVERT: B 164 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 200 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8608 (m) REVERT: B 212 ASP cc_start: 0.7280 (p0) cc_final: 0.6369 (p0) REVERT: B 215 GLU cc_start: 0.7988 (pm20) cc_final: 0.7616 (pm20) REVERT: B 219 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7390 (mmt90) REVERT: B 222 PHE cc_start: 0.8735 (m-80) cc_final: 0.8528 (m-80) REVERT: B 234 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: B 297 TRP cc_start: 0.8620 (m100) cc_final: 0.8342 (m100) REVERT: B 339 TRP cc_start: 0.9118 (m100) cc_final: 0.8645 (m-10) REVERT: C 32 LYS cc_start: 0.6197 (tppt) cc_final: 0.5666 (mttt) REVERT: R 83 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7403 (tm) REVERT: R 179 ARG cc_start: 0.9074 (ptm-80) cc_final: 0.8716 (ptm160) REVERT: R 251 CYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8321 (t) REVERT: R 293 TRP cc_start: 0.7872 (OUTLIER) cc_final: 0.6910 (m-10) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.2003 time to fit residues: 47.6742 Evaluate side-chains 188 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117721 restraints weight = 12018.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121693 restraints weight = 6684.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124432 restraints weight = 4329.376| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6943 Z= 0.209 Angle : 0.650 11.044 9427 Z= 0.322 Chirality : 0.043 0.179 1098 Planarity : 0.004 0.035 1189 Dihedral : 5.106 64.066 957 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.01 % Allowed : 24.32 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.30), residues: 875 helix: 0.54 (0.28), residues: 344 sheet: -2.01 (0.41), residues: 146 loop : -1.80 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.005 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8860 (t70) cc_final: 0.8146 (t0) REVERT: A 186 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8008 (mt-10) REVERT: A 198 MET cc_start: 0.8193 (mmp) cc_final: 0.7863 (mmp) REVERT: A 214 CYS cc_start: 0.9000 (t) cc_final: 0.8672 (m) REVERT: A 247 MET cc_start: 0.7854 (mtm) cc_final: 0.7512 (mtt) REVERT: A 276 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5245 (tp30) REVERT: A 310 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7589 (tp) REVERT: A 313 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8279 (mtp85) REVERT: B 164 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8792 (p) REVERT: B 169 TRP cc_start: 0.7891 (OUTLIER) cc_final: 0.6957 (m-90) REVERT: B 200 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8689 (m) REVERT: B 212 ASP cc_start: 0.7196 (p0) cc_final: 0.6453 (p0) REVERT: B 219 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7417 (tpp80) REVERT: B 222 PHE cc_start: 0.8769 (m-80) cc_final: 0.8544 (m-80) REVERT: B 234 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: B 297 TRP cc_start: 0.8679 (m100) cc_final: 0.8370 (m100) REVERT: B 339 TRP cc_start: 0.9124 (m100) cc_final: 0.8644 (m-10) REVERT: C 11 GLN cc_start: 0.6659 (pm20) cc_final: 0.5977 (tm-30) REVERT: C 32 LYS cc_start: 0.6233 (tppt) cc_final: 0.5706 (mttt) REVERT: R 83 LEU cc_start: 0.7644 (tm) cc_final: 0.7415 (tm) REVERT: R 179 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8725 (ptm160) REVERT: R 211 ARG cc_start: 0.6112 (mtt90) cc_final: 0.5854 (mtt90) REVERT: R 251 CYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8329 (t) REVERT: R 255 MET cc_start: 0.8660 (ttt) cc_final: 0.8437 (ttt) REVERT: R 293 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.6408 (m-10) outliers start: 35 outliers final: 20 residues processed: 183 average time/residue: 0.1961 time to fit residues: 47.0648 Evaluate side-chains 184 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 0.0020 chunk 3 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 overall best weight: 0.5086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119083 restraints weight = 12062.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123117 restraints weight = 6614.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125855 restraints weight = 4222.229| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6943 Z= 0.181 Angle : 0.651 11.842 9427 Z= 0.323 Chirality : 0.042 0.173 1098 Planarity : 0.004 0.037 1189 Dihedral : 5.050 66.180 957 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.43 % Allowed : 25.32 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.27 (0.30), residues: 875 helix: 0.59 (0.28), residues: 345 sheet: -1.94 (0.41), residues: 146 loop : -1.68 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE B 222 TYR 0.018 0.001 TYR R 149 ARG 0.008 0.001 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8625 (m-40) cc_final: 0.8021 (t0) REVERT: A 26 ASP cc_start: 0.8847 (t70) cc_final: 0.8130 (t0) REVERT: A 186 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 198 MET cc_start: 0.8309 (mmp) cc_final: 0.8013 (mmp) REVERT: A 214 CYS cc_start: 0.9035 (t) cc_final: 0.8675 (m) REVERT: A 247 MET cc_start: 0.7836 (mtm) cc_final: 0.7502 (mtt) REVERT: A 276 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5172 (tp30) REVERT: A 310 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7594 (tp) REVERT: A 313 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8264 (mtp85) REVERT: B 51 LEU cc_start: 0.9209 (mp) cc_final: 0.8998 (tp) REVERT: B 59 TYR cc_start: 0.8770 (m-80) cc_final: 0.8537 (m-80) REVERT: B 89 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8261 (mttp) REVERT: B 164 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 169 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.7081 (m-90) REVERT: B 200 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8691 (m) REVERT: B 212 ASP cc_start: 0.7103 (p0) cc_final: 0.6261 (p0) REVERT: B 234 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: B 297 TRP cc_start: 0.8627 (m100) cc_final: 0.8350 (m100) REVERT: B 339 TRP cc_start: 0.9122 (m100) cc_final: 0.8651 (m-10) REVERT: C 11 GLN cc_start: 0.6640 (pm20) cc_final: 0.5952 (tm-30) REVERT: C 18 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6193 (tm130) REVERT: C 32 LYS cc_start: 0.6133 (tppt) cc_final: 0.5619 (mttt) REVERT: R 83 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7407 (tm) REVERT: R 179 ARG cc_start: 0.9068 (ptm-80) cc_final: 0.8715 (ptm160) REVERT: R 255 MET cc_start: 0.8634 (ttt) cc_final: 0.8409 (ttt) REVERT: R 293 TRP cc_start: 0.7894 (OUTLIER) cc_final: 0.6935 (m-10) outliers start: 31 outliers final: 20 residues processed: 181 average time/residue: 0.1974 time to fit residues: 46.8182 Evaluate side-chains 186 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 18 GLN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119198 restraints weight = 11978.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123448 restraints weight = 6466.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126335 restraints weight = 4096.352| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6943 Z= 0.175 Angle : 0.633 9.056 9427 Z= 0.316 Chirality : 0.042 0.171 1098 Planarity : 0.004 0.036 1189 Dihedral : 5.016 66.813 957 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.58 % Allowed : 24.89 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.20 (0.30), residues: 875 helix: 0.66 (0.28), residues: 345 sheet: -1.95 (0.41), residues: 146 loop : -1.64 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.024 0.001 PHE B 222 TYR 0.028 0.001 TYR A 302 ARG 0.008 0.001 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.02 seconds wall clock time: 44 minutes 1.66 seconds (2641.66 seconds total)