Starting phenix.real_space_refine on Tue Feb 3 23:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wsx_66209/02_2026/9wsx_66209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wsx_66209/02_2026/9wsx_66209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wsx_66209/02_2026/9wsx_66209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wsx_66209/02_2026/9wsx_66209.map" model { file = "/net/cci-nas-00/data/ceres_data/9wsx_66209/02_2026/9wsx_66209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wsx_66209/02_2026/9wsx_66209.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 45 5.16 5 C 4878 2.51 5 N 1265 2.21 5 O 1429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7623 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2315 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2730 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 327} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "H" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1333 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'TYR:plan': 4, 'ASP:plan': 4, 'ARG:plan': 1, 'TRP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 104 Chain: "L" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1198 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 167} Chain breaks: 2 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 2, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Classifications: {'peptide': 4} Link IDs: {'PTRANS': 1, 'TRANS': 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.59, per 1000 atoms: 0.21 Number of scatterers: 7623 At special positions: 0 Unit cell: (153.45, 102.3, 88.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 6 15.00 O 1429 8.00 N 1265 7.00 C 4878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 223.2 milliseconds 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 14 sheets defined 27.5% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 65 through 96 removed outlier: 4.011A pdb=" N THR R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 119 Processing helix chain 'R' and resid 120 through 131 Processing helix chain 'R' and resid 136 through 171 Processing helix chain 'R' and resid 171 through 179 removed outlier: 4.194A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 195 Processing helix chain 'R' and resid 195 through 204 removed outlier: 3.668A pdb=" N GLY R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 224 through 241 removed outlier: 4.093A pdb=" N ASN R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 261 Processing helix chain 'R' and resid 271 through 306 removed outlier: 4.003A pdb=" N THR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 337 removed outlier: 4.309A pdb=" N HIS R 319 " --> pdb=" O THR R 315 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE R 322 " --> pdb=" O TRP R 318 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 351 Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.701A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.101A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing sheet with id=AA1, first strand: chain 'R' and resid 368 through 371 Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28 removed outlier: 3.760A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY C 141 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 26 through 28 removed outlier: 3.760A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS C 140 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 287 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 209 removed outlier: 4.177A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER C 330 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL C 228 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 231 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA7, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.648A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.648A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 130 through 133 removed outlier: 3.592A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS H 174 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 133 Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.655A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.721A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1170 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: 1.10 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1196 1.32 - 1.44: 2095 1.44 - 1.57: 4412 1.57 - 1.69: 22 1.69 - 1.81: 62 Bond restraints: 7787 Sorted by residual: bond pdb=" OG1 TPO R 367 " pdb=" P TPO R 367 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO R 366 " pdb=" P TPO R 366 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O2P TPO R 366 " pdb=" P TPO R 366 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3P TPO R 366 " pdb=" P TPO R 366 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O2P TPO R 367 " pdb=" P TPO R 367 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 7782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 10519 2.43 - 4.85: 109 4.85 - 7.28: 11 7.28 - 9.71: 3 9.71 - 12.13: 2 Bond angle restraints: 10644 Sorted by residual: angle pdb=" CB TPO R 366 " pdb=" OG1 TPO R 366 " pdb=" P TPO R 366 " ideal model delta sigma weight residual 119.31 107.18 12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CB TPO R 367 " pdb=" OG1 TPO R 367 " pdb=" P TPO R 367 " ideal model delta sigma weight residual 119.31 107.31 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C TYR P 1 " pdb=" N PRO P 2 " pdb=" CA PRO P 2 " ideal model delta sigma weight residual 119.85 115.84 4.01 1.01e+00 9.80e-01 1.57e+01 angle pdb=" N HIS R 319 " pdb=" CA HIS R 319 " pdb=" C HIS R 319 " ideal model delta sigma weight residual 111.36 115.35 -3.99 1.09e+00 8.42e-01 1.34e+01 angle pdb=" N TRP R 318 " pdb=" CA TRP R 318 " pdb=" C TRP R 318 " ideal model delta sigma weight residual 111.11 107.01 4.10 1.20e+00 6.94e-01 1.16e+01 ... (remaining 10639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4248 16.95 - 33.90: 306 33.90 - 50.85: 66 50.85 - 67.80: 9 67.80 - 84.75: 3 Dihedral angle restraints: 4632 sinusoidal: 1633 harmonic: 2999 Sorted by residual: dihedral pdb=" CG ARG C 236 " pdb=" CD ARG C 236 " pdb=" NE ARG C 236 " pdb=" CZ ARG C 236 " ideal model delta sinusoidal sigma weight residual -180.00 -137.41 -42.59 2 1.50e+01 4.44e-03 9.77e+00 dihedral pdb=" CG LYS C 322 " pdb=" CD LYS C 322 " pdb=" CE LYS C 322 " pdb=" NZ LYS C 322 " ideal model delta sinusoidal sigma weight residual -180.00 -121.15 -58.85 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ILE R 215 " pdb=" C ILE R 215 " pdb=" N ASP R 216 " pdb=" CA ASP R 216 " ideal model delta harmonic sigma weight residual -180.00 -164.85 -15.15 0 5.00e+00 4.00e-02 9.18e+00 ... (remaining 4629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 985 0.044 - 0.088: 202 0.088 - 0.131: 82 0.131 - 0.175: 5 0.175 - 0.219: 3 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA TYR P 1 " pdb=" N TYR P 1 " pdb=" C TYR P 1 " pdb=" CB TYR P 1 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA HIS R 319 " pdb=" N HIS R 319 " pdb=" C HIS R 319 " pdb=" CB HIS R 319 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU R 331 " pdb=" N LEU R 331 " pdb=" C LEU R 331 " pdb=" CB LEU R 331 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 1274 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 332 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO R 333 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 333 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 333 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 13 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO C 14 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 325 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C GLY R 325 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY R 325 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR R 326 " 0.012 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 665 2.75 - 3.28: 7193 3.28 - 3.82: 12246 3.82 - 4.36: 13865 4.36 - 4.90: 24919 Nonbonded interactions: 58888 Sorted by model distance: nonbonded pdb=" OD1 ASP C 204 " pdb=" OH TYR C 208 " model vdw 2.208 3.040 nonbonded pdb=" N VAL H 5 " pdb=" O SER H 28 " model vdw 2.267 3.120 nonbonded pdb=" O PRO H 133 " pdb=" OG SER L 122 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR R 299 " pdb=" OE1 GLN R 314 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR C 249 " pdb=" O ARG C 285 " model vdw 2.332 3.040 ... (remaining 58883 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 7791 Z= 0.223 Angle : 0.618 12.132 10650 Z= 0.311 Chirality : 0.043 0.219 1277 Planarity : 0.005 0.069 1328 Dihedral : 12.487 84.754 2681 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 992 helix: 1.51 (0.32), residues: 241 sheet: 0.16 (0.30), residues: 306 loop : -0.89 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 179 TYR 0.016 0.001 TYR R 299 PHE 0.018 0.001 PHE R 152 TRP 0.009 0.001 TRP R 228 HIS 0.005 0.001 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7787) covalent geometry : angle 0.61796 (10644) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.66822 ( 6) hydrogen bonds : bond 0.16860 ( 392) hydrogen bonds : angle 7.58704 ( 1170) Misc. bond : bond 0.10225 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: R 112 LEU cc_start: 0.7085 (tp) cc_final: 0.6883 (tp) REVERT: R 185 LYS cc_start: 0.7714 (mttp) cc_final: 0.6759 (mttm) REVERT: R 200 LEU cc_start: 0.7440 (mm) cc_final: 0.7190 (pp) REVERT: R 275 LEU cc_start: 0.7130 (tt) cc_final: 0.6928 (mt) REVERT: C 62 ARG cc_start: 0.6961 (ttm110) cc_final: 0.6583 (ttm-80) REVERT: L 117 PHE cc_start: 0.6883 (m-80) cc_final: 0.6672 (m-80) outliers start: 0 outliers final: 1 residues processed: 236 average time/residue: 0.3905 time to fit residues: 98.4742 Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 183 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** H 210 HIS ** 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 = 0.4116 r_free = 0.4116 target = 0.168823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122978 restraints weight = 10811.718| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.05 r_work: 0.3449 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7791 Z= 0.140 Angle : 0.663 13.923 10650 Z= 0.322 Chirality : 0.044 0.248 1277 Planarity : 0.005 0.057 1328 Dihedral : 5.091 58.907 1109 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.27 % Allowed : 15.74 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 992 helix: 1.96 (0.33), residues: 243 sheet: 0.43 (0.29), residues: 318 loop : -0.76 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 95 TYR 0.020 0.001 TYR R 96 PHE 0.025 0.002 PHE L 140 TRP 0.007 0.001 TRP R 228 HIS 0.003 0.001 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7787) covalent geometry : angle 0.66307 (10644) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.94550 ( 6) hydrogen bonds : bond 0.03558 ( 392) hydrogen bonds : angle 5.23419 ( 1170) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.4627 (tmm) cc_final: 0.4326 (ttm) REVERT: R 104 ASN cc_start: 0.8318 (m-40) cc_final: 0.7822 (m110) REVERT: R 185 LYS cc_start: 0.7766 (mttp) cc_final: 0.6725 (mmmt) REVERT: R 200 LEU cc_start: 0.7596 (mm) cc_final: 0.7314 (tp) REVERT: R 218 THR cc_start: 0.8081 (t) cc_final: 0.7821 (p) REVERT: R 280 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7670 (ttt180) REVERT: R 345 ARG cc_start: 0.7062 (ttp80) cc_final: 0.6819 (ttp80) REVERT: C 62 ARG cc_start: 0.6801 (ttm110) cc_final: 0.5962 (ttm-80) REVERT: C 177 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7705 (mtm-85) REVERT: C 228 VAL cc_start: 0.6857 (t) cc_final: 0.6506 (m) REVERT: C 229 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7234 (mmmt) REVERT: C 232 LYS cc_start: 0.7229 (pptt) cc_final: 0.7023 (ptpp) REVERT: C 290 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: L 117 PHE cc_start: 0.7077 (m-80) cc_final: 0.6859 (m-80) REVERT: L 140 PHE cc_start: 0.7068 (p90) cc_final: 0.5799 (p90) outliers start: 26 outliers final: 12 residues processed: 169 average time/residue: 0.4405 time to fit residues: 79.1903 Evaluate side-chains 133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 164 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 314 GLN R 332 ASN C 122 ASN C 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.158159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110178 restraints weight = 10535.180| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.03 r_work: 0.3268 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7791 Z= 0.177 Angle : 0.658 9.531 10650 Z= 0.329 Chirality : 0.045 0.185 1277 Planarity : 0.005 0.056 1328 Dihedral : 5.183 62.689 1107 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.53 % Allowed : 17.13 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 992 helix: 1.57 (0.31), residues: 246 sheet: 0.49 (0.29), residues: 320 loop : -0.60 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.018 0.002 TYR C 21 PHE 0.027 0.002 PHE H 105 TRP 0.009 0.001 TRP H 106 HIS 0.004 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7787) covalent geometry : angle 0.65716 (10644) SS BOND : bond 0.00420 ( 3) SS BOND : angle 1.26873 ( 6) hydrogen bonds : bond 0.03876 ( 392) hydrogen bonds : angle 4.97993 ( 1170) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.247 Fit side-chains REVERT: R 95 ARG cc_start: 0.6146 (ptm160) cc_final: 0.4638 (ptt180) REVERT: R 166 TYR cc_start: 0.8115 (t80) cc_final: 0.7907 (t80) REVERT: R 182 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7280 (ttp80) REVERT: R 185 LYS cc_start: 0.8060 (mttp) cc_final: 0.6792 (ptmt) REVERT: R 218 THR cc_start: 0.8093 (t) cc_final: 0.7832 (p) REVERT: R 257 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8114 (pp) REVERT: R 275 LEU cc_start: 0.6717 (tt) cc_final: 0.6497 (mt) REVERT: R 280 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7447 (mtt-85) REVERT: R 299 TYR cc_start: 0.7537 (t80) cc_final: 0.7203 (t80) REVERT: R 345 ARG cc_start: 0.7157 (ttp80) cc_final: 0.6822 (ttp80) REVERT: R 374 LYS cc_start: 0.7058 (mttt) cc_final: 0.6691 (tmtt) REVERT: C 46 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 62 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6207 (ttm-80) REVERT: C 165 ARG cc_start: 0.8596 (ptm160) cc_final: 0.8344 (ptp-170) REVERT: C 177 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7934 (mtm-85) REVERT: C 229 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7552 (mmmt) REVERT: C 232 LYS cc_start: 0.8071 (pptt) cc_final: 0.7751 (mtpt) REVERT: C 257 GLU cc_start: 0.8214 (pt0) cc_final: 0.7787 (tm-30) REVERT: H 24 SER cc_start: 0.9135 (t) cc_final: 0.8836 (p) REVERT: H 60 TYR cc_start: 0.8330 (m-10) cc_final: 0.7994 (m-10) REVERT: L 79 LEU cc_start: 0.7917 (tp) cc_final: 0.7660 (mt) REVERT: L 80 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8131 (mp10) REVERT: L 117 PHE cc_start: 0.7410 (m-80) cc_final: 0.7052 (m-80) outliers start: 36 outliers final: 14 residues processed: 174 average time/residue: 0.4642 time to fit residues: 85.5765 Evaluate side-chains 145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 317 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN R 109 ASN C 219 HIS H 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110675 restraints weight = 10488.677| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.04 r_work: 0.3274 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7791 Z= 0.145 Angle : 0.594 9.755 10650 Z= 0.296 Chirality : 0.043 0.169 1277 Planarity : 0.005 0.055 1328 Dihedral : 5.030 66.076 1107 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.29 % Allowed : 19.77 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.27), residues: 992 helix: 1.77 (0.31), residues: 246 sheet: 0.57 (0.28), residues: 317 loop : -0.48 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 22 TYR 0.016 0.001 TYR H 107 PHE 0.021 0.001 PHE H 105 TRP 0.007 0.001 TRP H 106 HIS 0.002 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7787) covalent geometry : angle 0.59308 (10644) SS BOND : bond 0.00563 ( 3) SS BOND : angle 1.22272 ( 6) hydrogen bonds : bond 0.03367 ( 392) hydrogen bonds : angle 4.69745 ( 1170) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.272 Fit side-chains REVERT: R 87 PHE cc_start: 0.7699 (m-10) cc_final: 0.7105 (m-80) REVERT: R 161 MET cc_start: 0.8178 (ttm) cc_final: 0.7872 (ttp) REVERT: R 166 TYR cc_start: 0.8095 (t80) cc_final: 0.7852 (t80) REVERT: R 174 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6605 (mtpt) REVERT: R 182 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7284 (ttp80) REVERT: R 185 LYS cc_start: 0.7908 (mttp) cc_final: 0.6884 (ptmt) REVERT: R 218 THR cc_start: 0.8039 (t) cc_final: 0.7818 (p) REVERT: R 257 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8141 (pp) REVERT: R 280 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7637 (ttt180) REVERT: R 299 TYR cc_start: 0.7781 (t80) cc_final: 0.7175 (t80) REVERT: R 314 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.5706 (tp40) REVERT: R 345 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7010 (ttp80) REVERT: R 374 LYS cc_start: 0.7185 (mttt) cc_final: 0.6878 (tmtt) REVERT: C 62 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6138 (ttm-80) REVERT: C 83 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8014 (t0) REVERT: C 155 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6523 (pp20) REVERT: C 165 ARG cc_start: 0.8608 (ptm160) cc_final: 0.8183 (ptp-170) REVERT: C 229 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7250 (mmmt) REVERT: C 232 LYS cc_start: 0.8249 (pptt) cc_final: 0.7893 (mtpt) REVERT: C 257 GLU cc_start: 0.8380 (pt0) cc_final: 0.7922 (tm-30) REVERT: H 60 TYR cc_start: 0.8494 (m-10) cc_final: 0.8049 (m-10) REVERT: L 79 LEU cc_start: 0.8003 (tp) cc_final: 0.7703 (mt) REVERT: L 80 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8124 (mp10) REVERT: L 117 PHE cc_start: 0.7385 (m-80) cc_final: 0.7058 (m-80) REVERT: P 1 TYR cc_start: 0.8380 (t80) cc_final: 0.8070 (t80) outliers start: 42 outliers final: 20 residues processed: 156 average time/residue: 0.4336 time to fit residues: 72.1413 Evaluate side-chains 138 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.0870 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN C 219 HIS H 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112285 restraints weight = 10424.193| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.01 r_work: 0.3294 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7791 Z= 0.115 Angle : 0.569 12.539 10650 Z= 0.280 Chirality : 0.042 0.184 1277 Planarity : 0.005 0.055 1328 Dihedral : 4.860 67.694 1107 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.65 % Allowed : 22.17 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.27), residues: 992 helix: 1.95 (0.32), residues: 247 sheet: 0.77 (0.29), residues: 317 loop : -0.39 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 95 TYR 0.014 0.001 TYR H 107 PHE 0.028 0.001 PHE L 140 TRP 0.006 0.001 TRP H 106 HIS 0.002 0.000 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7787) covalent geometry : angle 0.56919 (10644) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.96047 ( 6) hydrogen bonds : bond 0.03231 ( 392) hydrogen bonds : angle 4.51322 ( 1170) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.195 Fit side-chains REVERT: R 87 PHE cc_start: 0.7756 (m-10) cc_final: 0.7201 (m-80) REVERT: R 146 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7061 (tp) REVERT: R 161 MET cc_start: 0.8224 (ttm) cc_final: 0.7944 (ttp) REVERT: R 182 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7289 (ttp80) REVERT: R 185 LYS cc_start: 0.7860 (mttp) cc_final: 0.6909 (ptmt) REVERT: R 218 THR cc_start: 0.8015 (t) cc_final: 0.7703 (p) REVERT: R 257 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8177 (pp) REVERT: R 274 ASN cc_start: 0.7124 (m-40) cc_final: 0.6596 (m110) REVERT: R 277 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7883 (ttp-110) REVERT: R 280 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7650 (ttt180) REVERT: R 299 TYR cc_start: 0.7766 (t80) cc_final: 0.7180 (t80) REVERT: R 314 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.5683 (tp40) REVERT: R 345 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7055 (ttp80) REVERT: R 374 LYS cc_start: 0.7231 (mttt) cc_final: 0.6963 (tmtt) REVERT: C 62 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6087 (ttm-80) REVERT: C 83 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.7986 (t0) REVERT: C 155 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6517 (pp20) REVERT: C 165 ARG cc_start: 0.8574 (ptm160) cc_final: 0.8295 (ptp-170) REVERT: C 229 LYS cc_start: 0.7819 (mtmm) cc_final: 0.7375 (mmmt) REVERT: C 232 LYS cc_start: 0.8217 (pptt) cc_final: 0.7908 (mtpt) REVERT: C 257 GLU cc_start: 0.8381 (pt0) cc_final: 0.7919 (tm-30) REVERT: H 60 TYR cc_start: 0.8487 (m-10) cc_final: 0.7916 (m-10) REVERT: L 79 LEU cc_start: 0.8048 (tp) cc_final: 0.7746 (mt) REVERT: L 80 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8098 (mp10) REVERT: L 117 PHE cc_start: 0.7406 (m-80) cc_final: 0.7106 (m-80) REVERT: L 167 GLN cc_start: 0.7926 (mt0) cc_final: 0.7376 (mt0) outliers start: 29 outliers final: 19 residues processed: 150 average time/residue: 0.4373 time to fit residues: 69.9683 Evaluate side-chains 144 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 59 optimal weight: 0.0470 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.155553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107880 restraints weight = 10418.328| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.99 r_work: 0.3224 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7791 Z= 0.178 Angle : 0.624 11.522 10650 Z= 0.310 Chirality : 0.043 0.174 1277 Planarity : 0.005 0.054 1328 Dihedral : 5.041 67.175 1107 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.41 % Allowed : 21.54 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 992 helix: 1.87 (0.32), residues: 245 sheet: 0.83 (0.29), residues: 321 loop : -0.42 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 95 TYR 0.015 0.001 TYR H 107 PHE 0.028 0.002 PHE H 105 TRP 0.010 0.001 TRP H 106 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7787) covalent geometry : angle 0.62378 (10644) SS BOND : bond 0.00444 ( 3) SS BOND : angle 1.21574 ( 6) hydrogen bonds : bond 0.03518 ( 392) hydrogen bonds : angle 4.68642 ( 1170) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: R 87 PHE cc_start: 0.7915 (m-10) cc_final: 0.7378 (m-80) REVERT: R 146 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7170 (tp) REVERT: R 182 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7566 (ttp80) REVERT: R 185 LYS cc_start: 0.7912 (mttp) cc_final: 0.6987 (ptmt) REVERT: R 257 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8180 (pp) REVERT: R 277 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7827 (ptm160) REVERT: R 280 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7487 (mtt-85) REVERT: R 299 TYR cc_start: 0.7853 (t80) cc_final: 0.7467 (t80) REVERT: R 314 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.5795 (tp40) REVERT: C 46 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 62 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6357 (mtp85) REVERT: C 83 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8069 (t0) REVERT: C 155 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: C 157 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8184 (tptt) REVERT: C 160 LYS cc_start: 0.8189 (tttt) cc_final: 0.7883 (tttm) REVERT: C 165 ARG cc_start: 0.8679 (ptm160) cc_final: 0.8406 (ptp-170) REVERT: C 189 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: C 200 GLU cc_start: 0.7634 (tp30) cc_final: 0.7398 (tp30) REVERT: C 229 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7544 (mmpt) REVERT: C 232 LYS cc_start: 0.8182 (pptt) cc_final: 0.7938 (mtpt) REVERT: C 257 GLU cc_start: 0.8396 (pt0) cc_final: 0.7915 (tm-30) REVERT: L 79 LEU cc_start: 0.8131 (tp) cc_final: 0.7794 (mt) REVERT: L 80 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8006 (mp10) REVERT: L 167 GLN cc_start: 0.7791 (mt0) cc_final: 0.7241 (mt0) outliers start: 35 outliers final: 17 residues processed: 141 average time/residue: 0.4503 time to fit residues: 67.4835 Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 317 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108522 restraints weight = 10362.374| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.99 r_work: 0.3235 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7791 Z= 0.151 Angle : 0.603 10.675 10650 Z= 0.295 Chirality : 0.043 0.193 1277 Planarity : 0.005 0.054 1328 Dihedral : 4.973 69.558 1107 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.41 % Allowed : 21.91 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.27), residues: 992 helix: 1.88 (0.32), residues: 245 sheet: 0.87 (0.29), residues: 323 loop : -0.39 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 95 TYR 0.014 0.001 TYR H 107 PHE 0.030 0.002 PHE L 140 TRP 0.012 0.001 TRP P 3 HIS 0.002 0.001 HIS R 297 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7787) covalent geometry : angle 0.60221 (10644) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.31756 ( 6) hydrogen bonds : bond 0.03404 ( 392) hydrogen bonds : angle 4.57178 ( 1170) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.281 Fit side-chains REVERT: R 87 PHE cc_start: 0.7845 (m-10) cc_final: 0.7328 (m-80) REVERT: R 130 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.6064 (ptt) REVERT: R 146 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7095 (tp) REVERT: R 174 LYS cc_start: 0.7267 (mtpt) cc_final: 0.6904 (mttt) REVERT: R 185 LYS cc_start: 0.7790 (mttp) cc_final: 0.6963 (mtpt) REVERT: R 276 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7389 (mtp85) REVERT: R 277 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7878 (ptm160) REVERT: R 280 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7419 (mtt-85) REVERT: R 299 TYR cc_start: 0.7834 (t80) cc_final: 0.7470 (t80) REVERT: R 314 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.5747 (tp40) REVERT: R 345 ARG cc_start: 0.7436 (ttp80) cc_final: 0.7093 (ttp80) REVERT: C 46 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: C 62 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6033 (ttm-80) REVERT: C 155 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6682 (pp20) REVERT: C 157 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8206 (tptt) REVERT: C 165 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8436 (ptp-170) REVERT: C 189 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: C 200 GLU cc_start: 0.7726 (tp30) cc_final: 0.7222 (tp30) REVERT: C 229 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7645 (mmpt) REVERT: C 232 LYS cc_start: 0.8219 (pptt) cc_final: 0.7932 (mtpt) REVERT: C 257 GLU cc_start: 0.8390 (pt0) cc_final: 0.7875 (tm-30) REVERT: L 4 GLN cc_start: 0.8815 (mt0) cc_final: 0.8611 (tt0) REVERT: L 79 LEU cc_start: 0.8188 (tp) cc_final: 0.7850 (mt) REVERT: L 80 GLN cc_start: 0.8778 (mm-40) cc_final: 0.7995 (mp10) REVERT: L 167 GLN cc_start: 0.7769 (mt0) cc_final: 0.7213 (mt0) outliers start: 35 outliers final: 17 residues processed: 136 average time/residue: 0.4743 time to fit residues: 68.1325 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 130 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 317 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110788 restraints weight = 10493.279| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.98 r_work: 0.3266 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7791 Z= 0.114 Angle : 0.592 10.327 10650 Z= 0.286 Chirality : 0.042 0.186 1277 Planarity : 0.005 0.054 1328 Dihedral : 4.870 71.322 1107 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.53 % Allowed : 23.17 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 992 helix: 1.95 (0.32), residues: 247 sheet: 0.98 (0.29), residues: 323 loop : -0.31 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 182 TYR 0.014 0.001 TYR R 75 PHE 0.014 0.001 PHE H 105 TRP 0.008 0.001 TRP P 3 HIS 0.002 0.000 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7787) covalent geometry : angle 0.59006 (10644) SS BOND : bond 0.00538 ( 3) SS BOND : angle 1.91909 ( 6) hydrogen bonds : bond 0.03194 ( 392) hydrogen bonds : angle 4.39291 ( 1170) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.220 Fit side-chains REVERT: R 87 PHE cc_start: 0.7849 (m-10) cc_final: 0.7371 (m-80) REVERT: R 174 LYS cc_start: 0.7282 (mtpt) cc_final: 0.6916 (mttt) REVERT: R 185 LYS cc_start: 0.7856 (mttp) cc_final: 0.6997 (mtpt) REVERT: R 277 ARG cc_start: 0.8201 (ptm160) cc_final: 0.7961 (ptm160) REVERT: R 280 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7639 (ttt180) REVERT: R 345 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7114 (ttp80) REVERT: C 62 ARG cc_start: 0.7082 (ttm110) cc_final: 0.6238 (mtt-85) REVERT: C 83 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8193 (t0) REVERT: C 116 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8755 (m) REVERT: C 155 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6855 (pp20) REVERT: C 157 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8219 (tptt) REVERT: C 158 ILE cc_start: 0.8331 (pp) cc_final: 0.8055 (pt) REVERT: C 165 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8446 (ptp-170) REVERT: C 189 GLN cc_start: 0.7886 (pt0) cc_final: 0.7567 (mt0) REVERT: C 200 GLU cc_start: 0.7726 (tp30) cc_final: 0.7274 (tp30) REVERT: C 229 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7645 (mmpt) REVERT: C 232 LYS cc_start: 0.8188 (pptt) cc_final: 0.7946 (mtpt) REVERT: L 4 GLN cc_start: 0.8781 (mt0) cc_final: 0.8570 (tt0) REVERT: L 79 LEU cc_start: 0.8122 (tp) cc_final: 0.7803 (mt) REVERT: L 80 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8001 (mp10) REVERT: L 167 GLN cc_start: 0.7767 (mt0) cc_final: 0.7225 (mt0) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.4822 time to fit residues: 67.7039 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 317 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110290 restraints weight = 10442.740| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.97 r_work: 0.3260 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7791 Z= 0.121 Angle : 0.618 10.620 10650 Z= 0.294 Chirality : 0.042 0.186 1277 Planarity : 0.004 0.054 1328 Dihedral : 4.821 71.420 1107 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.40 % Allowed : 23.68 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 992 helix: 2.05 (0.32), residues: 247 sheet: 1.03 (0.29), residues: 323 loop : -0.29 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 22 TYR 0.012 0.001 TYR H 107 PHE 0.030 0.001 PHE L 140 TRP 0.009 0.001 TRP P 3 HIS 0.003 0.001 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7787) covalent geometry : angle 0.61653 (10644) SS BOND : bond 0.00305 ( 3) SS BOND : angle 1.61906 ( 6) hydrogen bonds : bond 0.03170 ( 392) hydrogen bonds : angle 4.37696 ( 1170) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.237 Fit side-chains REVERT: R 87 PHE cc_start: 0.7868 (m-10) cc_final: 0.7437 (m-80) REVERT: R 146 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6991 (tp) REVERT: R 174 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6914 (mttt) REVERT: R 185 LYS cc_start: 0.7827 (mttp) cc_final: 0.6894 (ptmt) REVERT: R 280 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7618 (ttt180) REVERT: R 299 TYR cc_start: 0.7717 (t80) cc_final: 0.7213 (t80) REVERT: R 345 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7113 (ttp80) REVERT: C 62 ARG cc_start: 0.7127 (ttm110) cc_final: 0.6268 (mtt-85) REVERT: C 155 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6858 (pp20) REVERT: C 157 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8241 (tptt) REVERT: C 165 ARG cc_start: 0.8688 (ptm160) cc_final: 0.8308 (ptp-170) REVERT: C 189 GLN cc_start: 0.7885 (pt0) cc_final: 0.7625 (mt0) REVERT: C 229 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7655 (mmpt) REVERT: C 232 LYS cc_start: 0.8203 (pptt) cc_final: 0.7942 (mtpt) REVERT: L 79 LEU cc_start: 0.8129 (tp) cc_final: 0.7835 (mt) REVERT: L 80 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8027 (mp10) REVERT: L 167 GLN cc_start: 0.7774 (mt0) cc_final: 0.7223 (mt0) outliers start: 27 outliers final: 19 residues processed: 129 average time/residue: 0.4562 time to fit residues: 62.4834 Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 317 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 0.0030 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111371 restraints weight = 10323.979| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.96 r_work: 0.3275 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7791 Z= 0.112 Angle : 0.600 10.258 10650 Z= 0.291 Chirality : 0.042 0.175 1277 Planarity : 0.004 0.054 1328 Dihedral : 4.760 72.132 1107 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.77 % Allowed : 24.06 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 992 helix: 1.99 (0.33), residues: 248 sheet: 1.06 (0.29), residues: 323 loop : -0.31 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 22 TYR 0.012 0.001 TYR H 107 PHE 0.014 0.001 PHE H 105 TRP 0.008 0.001 TRP P 3 HIS 0.003 0.001 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7787) covalent geometry : angle 0.59915 (10644) SS BOND : bond 0.00250 ( 3) SS BOND : angle 1.45422 ( 6) hydrogen bonds : bond 0.03132 ( 392) hydrogen bonds : angle 4.37314 ( 1170) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.206 Fit side-chains REVERT: R 72 MET cc_start: 0.7972 (mtp) cc_final: 0.7735 (tpp) REVERT: R 87 PHE cc_start: 0.7887 (m-10) cc_final: 0.7449 (m-80) REVERT: R 146 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6854 (tp) REVERT: R 174 LYS cc_start: 0.7273 (mtpt) cc_final: 0.6905 (mttt) REVERT: R 185 LYS cc_start: 0.7841 (mttp) cc_final: 0.6929 (ptmt) REVERT: R 277 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7723 (ttp-110) REVERT: R 299 TYR cc_start: 0.7687 (t80) cc_final: 0.7205 (t80) REVERT: R 345 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7129 (ttp80) REVERT: C 62 ARG cc_start: 0.7120 (ttm110) cc_final: 0.6266 (mtt-85) REVERT: C 116 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8747 (m) REVERT: C 155 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6877 (pp20) REVERT: C 157 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (tptt) REVERT: C 165 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8313 (ptp-170) REVERT: C 189 GLN cc_start: 0.7888 (pt0) cc_final: 0.7612 (mt0) REVERT: C 229 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7654 (mmpt) REVERT: C 232 LYS cc_start: 0.8169 (pptt) cc_final: 0.7924 (mtpt) REVERT: L 79 LEU cc_start: 0.8138 (tp) cc_final: 0.7853 (mt) REVERT: L 80 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8010 (mp10) REVERT: L 167 GLN cc_start: 0.7774 (mt0) cc_final: 0.7220 (mt0) outliers start: 22 outliers final: 16 residues processed: 131 average time/residue: 0.4585 time to fit residues: 63.7091 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 317 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.158477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111953 restraints weight = 10432.488| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.99 r_work: 0.3290 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7791 Z= 0.106 Angle : 0.609 10.091 10650 Z= 0.291 Chirality : 0.042 0.178 1277 Planarity : 0.004 0.054 1328 Dihedral : 4.692 72.555 1107 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.02 % Allowed : 24.18 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.27), residues: 992 helix: 2.13 (0.33), residues: 248 sheet: 1.11 (0.29), residues: 323 loop : -0.30 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 22 TYR 0.012 0.001 TYR R 75 PHE 0.030 0.001 PHE L 140 TRP 0.010 0.001 TRP H 106 HIS 0.003 0.000 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7787) covalent geometry : angle 0.60821 (10644) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.36375 ( 6) hydrogen bonds : bond 0.03068 ( 392) hydrogen bonds : angle 4.30111 ( 1170) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.26 seconds wall clock time: 45 minutes 8.43 seconds (2708.43 seconds total)