Starting phenix.real_space_refine on Sun Aug 24 03:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmf_41387/08_2025/8tmf_41387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmf_41387/08_2025/8tmf_41387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmf_41387/08_2025/8tmf_41387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmf_41387/08_2025/8tmf_41387.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmf_41387/08_2025/8tmf_41387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmf_41387/08_2025/8tmf_41387.cif" } resolution = 3.4 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic. 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 Mg 2 5.21 5 S 59 5.16 5 C 10481 2.51 5 N 2623 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16127 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 983 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2879 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "E" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.94, per 1000 atoms: 0.31 Number of scatterers: 16127 At special positions: 0 Unit cell: (119.616, 144.18, 139.908, 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 59 16.00 Mg 2 11.99 O 2962 8.00 N 2623 7.00 C 10481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 799.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 53.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 31 through 34 removed outlier: 3.501A pdb=" N TYR H 34 " --> pdb=" O ASN H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 34' Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.556A pdb=" N SER A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 69 through 80 removed outlier: 4.103A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.580A pdb=" N LEU A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.527A pdb=" N LYS A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.592A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 3.930A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 4.128A pdb=" N ASP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 281 Processing helix chain 'A' and resid 283 through 300 removed outlier: 3.536A pdb=" N ILE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 326 through 347 removed outlier: 4.086A pdb=" N VAL A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.575A pdb=" N SER B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.714A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 56 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.798A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 200 removed outlier: 3.551A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 247 through 311 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 348 Processing helix chain 'C' and resid 69 through 81 removed outlier: 4.269A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.842A pdb=" N LEU C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 166 through 202 Processing helix chain 'C' and resid 204 through 236 removed outlier: 4.343A pdb=" N VAL C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 3.566A pdb=" N TYR C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 311 removed outlier: 3.521A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.937A pdb=" N VAL D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 4.025A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.519A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 238 removed outlier: 4.301A pdb=" N VAL D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 311 removed outlier: 4.091A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 348 removed outlier: 4.082A pdb=" N VAL D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 removed outlier: 3.743A pdb=" N SER E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.763A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.889A pdb=" N LYS E 164 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.609A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 237 removed outlier: 3.792A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Proline residue: E 227 - end of helix removed outlier: 3.782A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 311 removed outlier: 4.066A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix removed outlier: 3.588A pdb=" N TYR E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 349 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.541A pdb=" N THR L 23 " --> pdb=" O SER L 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.864A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.571A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.799A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 63 removed outlier: 7.094A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS H 99 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP H 119 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG H 101 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 63 removed outlier: 7.094A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 40 through 44 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44 removed outlier: 6.570A pdb=" N THR B 60 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET B 138 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 62 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN B 140 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 64 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 107 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.575A pdb=" N TRP C 61 " --> pdb=" O MET C 32 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 128 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 125 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 127 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 108 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 131 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 106 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.525A pdb=" N PHE D 42 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 28 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 121 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.643A pdb=" N ILE E 130 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP E 116 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E 114 " --> pdb=" O GLU E 123 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2850 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: 3.38 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.21: 1 1.21 - 1.36: 5123 1.36 - 1.51: 4629 1.51 - 1.66: 6630 1.66 - 1.81: 109 Bond restraints: 16492 Sorted by residual: bond pdb=" CG PRO C 59 " pdb=" CD PRO C 59 " ideal model delta sigma weight residual 1.503 1.055 0.448 3.40e-02 8.65e+02 1.74e+02 bond pdb=" N PRO C 59 " pdb=" CD PRO C 59 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" CB PRO C 59 " pdb=" CG PRO C 59 " ideal model delta sigma weight residual 1.492 1.311 0.181 5.00e-02 4.00e+02 1.31e+01 bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CG PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.503 1.446 0.057 3.40e-02 8.65e+02 2.81e+00 ... (remaining 16487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.30: 22343 6.30 - 12.59: 17 12.59 - 18.89: 0 18.89 - 25.18: 1 25.18 - 31.48: 2 Bond angle restraints: 22363 Sorted by residual: angle pdb=" N PRO C 59 " pdb=" CD PRO C 59 " pdb=" CG PRO C 59 " ideal model delta sigma weight residual 103.20 75.89 27.31 1.50e+00 4.44e-01 3.31e+02 angle pdb=" CA PRO C 59 " pdb=" CB PRO C 59 " pdb=" CG PRO C 59 " ideal model delta sigma weight residual 104.50 81.99 22.51 1.90e+00 2.77e-01 1.40e+02 angle pdb=" CB PRO C 59 " pdb=" CG PRO C 59 " pdb=" CD PRO C 59 " ideal model delta sigma weight residual 106.10 137.58 -31.48 3.20e+00 9.77e-02 9.68e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 111.67 118.73 -7.06 9.20e-01 1.18e+00 5.89e+01 angle pdb=" CA PRO C 59 " pdb=" N PRO C 59 " pdb=" CD PRO C 59 " ideal model delta sigma weight residual 112.00 101.76 10.24 1.40e+00 5.10e-01 5.35e+01 ... (remaining 22358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 8725 17.56 - 35.12: 979 35.12 - 52.69: 167 52.69 - 70.25: 26 70.25 - 87.81: 17 Dihedral angle restraints: 9914 sinusoidal: 4122 harmonic: 5792 Sorted by residual: dihedral pdb=" N PRO C 59 " pdb=" CG PRO C 59 " pdb=" CD PRO C 59 " pdb=" CB PRO C 59 " ideal model delta sinusoidal sigma weight residual 30.00 82.53 -52.53 1 1.50e+01 4.44e-03 1.67e+01 dihedral pdb=" CA TRP D 325 " pdb=" C TRP D 325 " pdb=" N GLY D 326 " pdb=" CA GLY D 326 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ILE D 300 " pdb=" C ILE D 300 " pdb=" N PHE D 301 " pdb=" CA PHE D 301 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1663 0.033 - 0.067: 574 0.067 - 0.100: 226 0.100 - 0.134: 72 0.134 - 0.167: 9 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CG LEU D 185 " pdb=" CB LEU D 185 " pdb=" CD1 LEU D 185 " pdb=" CD2 LEU D 185 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CB ILE E 160 " pdb=" CA ILE E 160 " pdb=" CG1 ILE E 160 " pdb=" CG2 ILE E 160 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB ILE E 36 " pdb=" CA ILE E 36 " pdb=" CG1 ILE E 36 " pdb=" CG2 ILE E 36 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 2541 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 302 " 0.093 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO B 303 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 303 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO B 303 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 58 " -0.048 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO C 59 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 327 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 328 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " -0.029 5.00e-02 4.00e+02 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 343 2.70 - 3.25: 16090 3.25 - 3.80: 25610 3.80 - 4.35: 31966 4.35 - 4.90: 54283 Nonbonded interactions: 128292 Sorted by model distance: nonbonded pdb=" O LYS E 111 " pdb=" OH TYR E 181 " model vdw 2.151 3.040 nonbonded pdb=" O GLU B 204 " pdb=" OG1 THR B 207 " model vdw 2.185 3.040 nonbonded pdb=" O THR A 295 " pdb=" OG1 THR A 299 " model vdw 2.200 3.040 nonbonded pdb=" O GLU B 246 " pdb=" OG1 THR B 247 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASN B 33 " pdb=" OG1 THR B 58 " model vdw 2.235 3.040 ... (remaining 128287 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 351) selection = (chain 'B' and resid 17 through 351) selection = chain 'C' selection = (chain 'D' and resid 17 through 351) selection = (chain 'E' and resid 17 through 351) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.090 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.005 0.448 16494 Z= 0.179 Angle : 0.667 31.478 22367 Z= 0.354 Chirality : 0.042 0.167 2544 Planarity : 0.005 0.136 2796 Dihedral : 14.837 87.808 6164 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.42 (0.20), residues: 1939 helix: 2.48 (0.17), residues: 952 sheet: 0.70 (0.30), residues: 365 loop : -1.46 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 229 TYR 0.021 0.001 TYR E 236 PHE 0.019 0.001 PHE E 39 TRP 0.008 0.001 TRP D 226 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00494 (16492) covalent geometry : angle 0.66721 (22363) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.72927 ( 4) hydrogen bonds : bond 0.15120 ( 970) hydrogen bonds : angle 6.44416 ( 2850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8257 (m-80) cc_final: 0.7943 (m-80) REVERT: H 117 ASP cc_start: 0.7584 (m-30) cc_final: 0.7285 (m-30) REVERT: A 202 ARG cc_start: 0.6592 (ttp80) cc_final: 0.6274 (tmt-80) REVERT: B 89 ASP cc_start: 0.6818 (m-30) cc_final: 0.6366 (m-30) REVERT: B 116 ASP cc_start: 0.7474 (t0) cc_final: 0.6957 (t0) REVERT: B 158 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7430 (mtp85) REVERT: D 140 GLN cc_start: 0.5855 (mp10) cc_final: 0.5516 (mp10) REVERT: D 145 ASP cc_start: 0.4853 (p0) cc_final: 0.4600 (p0) REVERT: E 54 ARG cc_start: 0.6743 (ptt90) cc_final: 0.6447 (ptt90) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.1230 time to fit residues: 71.8364 Evaluate side-chains 331 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** 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 = 0.4127 r_free = 0.4127 target = 0.205964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.165450 restraints weight = 20326.191| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.78 r_work: 0.3432 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16494 Z= 0.196 Angle : 0.619 8.286 22367 Z= 0.325 Chirality : 0.045 0.180 2544 Planarity : 0.005 0.088 2796 Dihedral : 4.310 21.956 2164 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.87 % Allowed : 11.67 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.18 (0.20), residues: 1939 helix: 2.26 (0.16), residues: 956 sheet: 0.66 (0.28), residues: 374 loop : -1.65 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.032 0.002 TYR B 236 PHE 0.029 0.002 PHE E 147 TRP 0.010 0.001 TRP H 104 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00465 (16492) covalent geometry : angle 0.61854 (22363) SS BOND : bond 0.00368 ( 2) SS BOND : angle 1.11837 ( 4) hydrogen bonds : bond 0.05894 ( 970) hydrogen bonds : angle 5.01559 ( 2850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 356 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7279 (ttp-110) REVERT: A 202 ARG cc_start: 0.6921 (ttp80) cc_final: 0.6564 (tmt-80) REVERT: A 313 MET cc_start: 0.7230 (mtp) cc_final: 0.6972 (mtp) REVERT: B 89 ASP cc_start: 0.7666 (m-30) cc_final: 0.7322 (m-30) REVERT: B 116 ASP cc_start: 0.7453 (t0) cc_final: 0.6599 (t0) REVERT: B 158 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7915 (mtp85) REVERT: C 191 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7403 (mm-30) REVERT: C 216 ARG cc_start: 0.6585 (mmm160) cc_final: 0.5883 (mmm160) REVERT: D 121 GLU cc_start: 0.6712 (mp0) cc_final: 0.6453 (mp0) REVERT: D 140 GLN cc_start: 0.6654 (mp10) cc_final: 0.5997 (mp10) REVERT: D 145 ASP cc_start: 0.4921 (p0) cc_final: 0.4631 (p0) REVERT: D 180 ASP cc_start: 0.7517 (t70) cc_final: 0.6501 (t0) REVERT: D 228 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8344 (mp) REVERT: D 233 SER cc_start: 0.7571 (m) cc_final: 0.6989 (m) REVERT: E 54 ARG cc_start: 0.6933 (ptt90) cc_final: 0.6644 (ptt90) REVERT: E 133 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7742 (mmmt) outliers start: 34 outliers final: 22 residues processed: 368 average time/residue: 0.1254 time to fit residues: 69.9212 Evaluate side-chains 368 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 284 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 25 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN D 33 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.203958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.163518 restraints weight = 20227.847| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.84 r_work: 0.3396 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16494 Z= 0.215 Angle : 0.605 8.821 22367 Z= 0.321 Chirality : 0.045 0.193 2544 Planarity : 0.005 0.075 2796 Dihedral : 4.355 22.395 2164 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.42 % Allowed : 15.31 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 0.96 (0.19), residues: 1939 helix: 2.12 (0.16), residues: 957 sheet: 0.39 (0.29), residues: 360 loop : -1.64 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 229 TYR 0.032 0.002 TYR B 236 PHE 0.021 0.002 PHE E 147 TRP 0.009 0.001 TRP H 104 HIS 0.005 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00514 (16492) covalent geometry : angle 0.60511 (22363) SS BOND : bond 0.00432 ( 2) SS BOND : angle 1.43545 ( 4) hydrogen bonds : bond 0.06005 ( 970) hydrogen bonds : angle 4.88150 ( 2850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 348 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7238 (ttp-110) REVERT: A 202 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6624 (tmt-80) REVERT: B 89 ASP cc_start: 0.7628 (m-30) cc_final: 0.7190 (m-30) REVERT: B 116 ASP cc_start: 0.7553 (t0) cc_final: 0.6956 (t70) REVERT: C 191 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 216 ARG cc_start: 0.6608 (mmm160) cc_final: 0.5916 (mmm160) REVERT: D 40 ARG cc_start: 0.6645 (mtt-85) cc_final: 0.6282 (mpp80) REVERT: D 100 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: D 140 GLN cc_start: 0.6788 (mp10) cc_final: 0.5484 (mp10) REVERT: D 145 ASP cc_start: 0.5066 (p0) cc_final: 0.4784 (p0) REVERT: D 180 ASP cc_start: 0.7575 (t70) cc_final: 0.6553 (t0) REVERT: D 206 GLU cc_start: 0.7198 (pm20) cc_final: 0.6980 (pm20) REVERT: D 228 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8343 (mp) REVERT: D 233 SER cc_start: 0.7670 (m) cc_final: 0.7134 (m) REVERT: E 54 ARG cc_start: 0.6922 (ptt90) cc_final: 0.6604 (ptt90) REVERT: E 133 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7829 (mmmt) outliers start: 44 outliers final: 31 residues processed: 371 average time/residue: 0.1251 time to fit residues: 70.3769 Evaluate side-chains 373 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 340 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 179 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 163 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** 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 = 0.4129 r_free = 0.4129 target = 0.206253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.165548 restraints weight = 20355.299| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.72 r_work: 0.3433 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16494 Z= 0.146 Angle : 0.552 9.820 22367 Z= 0.291 Chirality : 0.043 0.147 2544 Planarity : 0.004 0.065 2796 Dihedral : 4.185 20.794 2164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.86 % Allowed : 17.73 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.18 (0.20), residues: 1939 helix: 2.33 (0.16), residues: 959 sheet: 0.54 (0.29), residues: 352 loop : -1.60 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.032 0.001 TYR B 236 PHE 0.022 0.001 PHE E 147 TRP 0.009 0.001 TRP H 104 HIS 0.005 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00329 (16492) covalent geometry : angle 0.55157 (22363) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.05442 ( 4) hydrogen bonds : bond 0.05423 ( 970) hydrogen bonds : angle 4.61736 ( 2850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7154 (ttp-110) REVERT: A 202 ARG cc_start: 0.6951 (ttp80) cc_final: 0.6674 (tmt-80) REVERT: B 89 ASP cc_start: 0.7575 (m-30) cc_final: 0.7131 (m-30) REVERT: B 116 ASP cc_start: 0.7463 (t0) cc_final: 0.6833 (t0) REVERT: B 291 MET cc_start: 0.7896 (tpp) cc_final: 0.7500 (mmt) REVERT: B 341 MET cc_start: 0.5920 (mmt) cc_final: 0.5530 (mmt) REVERT: C 191 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 216 ARG cc_start: 0.6484 (mmm160) cc_final: 0.5814 (mmm160) REVERT: D 121 GLU cc_start: 0.6692 (mp0) cc_final: 0.6388 (mp0) REVERT: D 140 GLN cc_start: 0.6808 (mp10) cc_final: 0.5555 (mp10) REVERT: D 145 ASP cc_start: 0.5176 (p0) cc_final: 0.4849 (p0) REVERT: D 180 ASP cc_start: 0.7503 (t70) cc_final: 0.6501 (t0) REVERT: D 233 SER cc_start: 0.7533 (m) cc_final: 0.7023 (m) REVERT: D 279 TYR cc_start: 0.8730 (t80) cc_final: 0.8493 (t80) REVERT: E 54 ARG cc_start: 0.6915 (ptt90) cc_final: 0.6605 (ptt90) REVERT: E 120 HIS cc_start: 0.6427 (m-70) cc_final: 0.6221 (m170) REVERT: E 126 GLN cc_start: 0.8338 (tt0) cc_final: 0.8124 (tt0) REVERT: E 133 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7815 (mmmt) outliers start: 52 outliers final: 35 residues processed: 378 average time/residue: 0.1279 time to fit residues: 73.5708 Evaluate side-chains 371 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 336 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 126 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 147 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 157 optimal weight: 0.1980 chunk 94 optimal weight: 20.0000 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 80 ASN C 314 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.205518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.164686 restraints weight = 20435.755| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.86 r_work: 0.3418 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16494 Z= 0.169 Angle : 0.572 9.799 22367 Z= 0.299 Chirality : 0.044 0.181 2544 Planarity : 0.005 0.063 2796 Dihedral : 4.228 20.853 2164 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.47 % Allowed : 18.23 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.11 (0.20), residues: 1939 helix: 2.28 (0.16), residues: 959 sheet: 0.44 (0.29), residues: 356 loop : -1.64 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.032 0.001 TYR B 236 PHE 0.020 0.001 PHE E 147 TRP 0.016 0.001 TRP B 226 HIS 0.004 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00395 (16492) covalent geometry : angle 0.57175 (22363) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.22532 ( 4) hydrogen bonds : bond 0.05506 ( 970) hydrogen bonds : angle 4.59330 ( 2850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7211 (ttp-110) REVERT: A 202 ARG cc_start: 0.6897 (ttp80) cc_final: 0.6630 (tmt-80) REVERT: A 232 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8193 (mm) REVERT: B 89 ASP cc_start: 0.7604 (m-30) cc_final: 0.7162 (m-30) REVERT: B 116 ASP cc_start: 0.7465 (t0) cc_final: 0.6791 (t0) REVERT: B 145 ASP cc_start: 0.7656 (p0) cc_final: 0.7439 (p0) REVERT: B 291 MET cc_start: 0.8113 (tpp) cc_final: 0.7614 (mmt) REVERT: B 304 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 341 MET cc_start: 0.5923 (mmt) cc_final: 0.5584 (mmt) REVERT: C 191 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 216 ARG cc_start: 0.6493 (mmm160) cc_final: 0.5820 (mmm160) REVERT: D 100 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: D 103 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8039 (tm-30) REVERT: D 125 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5788 (tm-30) REVERT: D 140 GLN cc_start: 0.6705 (mp10) cc_final: 0.5457 (mp10) REVERT: D 145 ASP cc_start: 0.5143 (p0) cc_final: 0.4824 (p0) REVERT: D 233 SER cc_start: 0.7607 (m) cc_final: 0.7105 (m) REVERT: E 54 ARG cc_start: 0.6946 (ptt90) cc_final: 0.6612 (ptt90) REVERT: E 126 GLN cc_start: 0.8330 (tt0) cc_final: 0.8100 (tt0) REVERT: E 133 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7834 (mmmt) outliers start: 63 outliers final: 45 residues processed: 373 average time/residue: 0.1153 time to fit residues: 65.6502 Evaluate side-chains 375 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.204453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.163989 restraints weight = 20115.197| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.66 r_work: 0.3415 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16494 Z= 0.181 Angle : 0.579 8.621 22367 Z= 0.305 Chirality : 0.044 0.160 2544 Planarity : 0.005 0.062 2796 Dihedral : 4.282 21.310 2164 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.69 % Allowed : 19.22 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1939 helix: 2.23 (0.16), residues: 960 sheet: 0.31 (0.29), residues: 366 loop : -1.75 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.032 0.002 TYR B 236 PHE 0.019 0.001 PHE E 147 TRP 0.012 0.001 TRP B 226 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00429 (16492) covalent geometry : angle 0.57918 (22363) SS BOND : bond 0.00323 ( 2) SS BOND : angle 1.20840 ( 4) hydrogen bonds : bond 0.05627 ( 970) hydrogen bonds : angle 4.58863 ( 2850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7525 (ttm110) cc_final: 0.7141 (ttp-110) REVERT: A 202 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6709 (tmt-80) REVERT: A 232 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8182 (mm) REVERT: A 291 MET cc_start: 0.6918 (mmp) cc_final: 0.6617 (mmp) REVERT: B 30 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: B 89 ASP cc_start: 0.7634 (m-30) cc_final: 0.7205 (m-30) REVERT: B 116 ASP cc_start: 0.7536 (t0) cc_final: 0.6895 (t0) REVERT: B 145 ASP cc_start: 0.7714 (p0) cc_final: 0.7389 (p0) REVERT: B 304 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 116 ASP cc_start: 0.7902 (p0) cc_final: 0.7382 (p0) REVERT: C 175 ASP cc_start: 0.6511 (m-30) cc_final: 0.6185 (m-30) REVERT: C 191 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7377 (mm-30) REVERT: C 216 ARG cc_start: 0.6496 (mmm160) cc_final: 0.5843 (mmm160) REVERT: D 100 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6467 (pm20) REVERT: D 103 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 121 GLU cc_start: 0.6733 (mp0) cc_final: 0.6522 (mp0) REVERT: D 140 GLN cc_start: 0.6672 (mp10) cc_final: 0.5402 (mp10) REVERT: D 145 ASP cc_start: 0.5103 (p0) cc_final: 0.4804 (p0) REVERT: D 180 ASP cc_start: 0.7655 (t70) cc_final: 0.6575 (t0) REVERT: D 233 SER cc_start: 0.7630 (m) cc_final: 0.7149 (m) REVERT: E 54 ARG cc_start: 0.6934 (ptt90) cc_final: 0.6612 (ptt90) REVERT: E 88 GLU cc_start: 0.5540 (pp20) cc_final: 0.5143 (pp20) REVERT: E 126 GLN cc_start: 0.8333 (tt0) cc_final: 0.8098 (tt0) REVERT: E 133 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7849 (mmmt) REVERT: E 181 TYR cc_start: 0.7590 (m-80) cc_final: 0.7335 (m-80) outliers start: 67 outliers final: 52 residues processed: 378 average time/residue: 0.1081 time to fit residues: 62.6993 Evaluate side-chains 388 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 332 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 318 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 174 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN B 33 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.204368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.164004 restraints weight = 20021.473| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.68 r_work: 0.3415 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16494 Z= 0.181 Angle : 0.580 9.192 22367 Z= 0.305 Chirality : 0.044 0.162 2544 Planarity : 0.005 0.061 2796 Dihedral : 4.297 21.685 2164 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.07 % Allowed : 19.88 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 0.99 (0.19), residues: 1939 helix: 2.22 (0.16), residues: 962 sheet: 0.31 (0.29), residues: 365 loop : -1.75 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.032 0.002 TYR B 236 PHE 0.019 0.001 PHE E 147 TRP 0.008 0.001 TRP H 119 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00429 (16492) covalent geometry : angle 0.57960 (22363) SS BOND : bond 0.00335 ( 2) SS BOND : angle 1.19771 ( 4) hydrogen bonds : bond 0.05642 ( 970) hydrogen bonds : angle 4.57176 ( 2850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 333 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7165 (ttp-110) REVERT: A 232 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8182 (mm) REVERT: A 291 MET cc_start: 0.7108 (mmp) cc_final: 0.6813 (mmp) REVERT: B 30 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: B 89 ASP cc_start: 0.7566 (m-30) cc_final: 0.7193 (m-30) REVERT: B 116 ASP cc_start: 0.7640 (t0) cc_final: 0.6986 (t0) REVERT: B 133 LYS cc_start: 0.7508 (ttmt) cc_final: 0.7210 (ttmm) REVERT: B 145 ASP cc_start: 0.7715 (p0) cc_final: 0.7354 (p0) REVERT: B 304 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 341 MET cc_start: 0.5968 (mmt) cc_final: 0.5595 (mmt) REVERT: C 191 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 216 ARG cc_start: 0.6493 (mmm160) cc_final: 0.5906 (mmm160) REVERT: D 100 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6496 (pm20) REVERT: D 140 GLN cc_start: 0.6480 (mp10) cc_final: 0.5321 (mp10) REVERT: D 145 ASP cc_start: 0.5111 (p0) cc_final: 0.4804 (p0) REVERT: D 180 ASP cc_start: 0.7593 (t70) cc_final: 0.6585 (t0) REVERT: D 233 SER cc_start: 0.7590 (m) cc_final: 0.7122 (m) REVERT: E 54 ARG cc_start: 0.6946 (ptt90) cc_final: 0.6618 (ptt90) REVERT: E 88 GLU cc_start: 0.5516 (pp20) cc_final: 0.5201 (pp20) REVERT: E 133 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7877 (mmmt) REVERT: E 181 TYR cc_start: 0.7597 (m-80) cc_final: 0.7325 (m-80) REVERT: E 291 MET cc_start: 0.7703 (ttt) cc_final: 0.7499 (ttm) outliers start: 74 outliers final: 60 residues processed: 379 average time/residue: 0.1035 time to fit residues: 60.2305 Evaluate side-chains 386 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 318 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS E 126 GLN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.204526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.164761 restraints weight = 20069.486| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.78 r_work: 0.3420 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16494 Z= 0.177 Angle : 0.580 8.672 22367 Z= 0.306 Chirality : 0.044 0.160 2544 Planarity : 0.005 0.061 2796 Dihedral : 4.303 21.543 2164 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.80 % Allowed : 20.21 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.01 (0.19), residues: 1939 helix: 2.22 (0.16), residues: 959 sheet: 0.39 (0.29), residues: 359 loop : -1.73 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.032 0.002 TYR B 236 PHE 0.018 0.001 PHE E 147 TRP 0.007 0.001 TRP H 104 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00417 (16492) covalent geometry : angle 0.58023 (22363) SS BOND : bond 0.00320 ( 2) SS BOND : angle 1.17234 ( 4) hydrogen bonds : bond 0.05615 ( 970) hydrogen bonds : angle 4.54999 ( 2850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7219 (ttp-110) REVERT: A 120 HIS cc_start: 0.6772 (m170) cc_final: 0.6417 (m170) REVERT: A 232 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (mm) REVERT: A 291 MET cc_start: 0.7044 (mmp) cc_final: 0.6801 (mmp) REVERT: B 30 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: B 89 ASP cc_start: 0.7524 (m-30) cc_final: 0.7157 (m-30) REVERT: B 116 ASP cc_start: 0.7677 (t0) cc_final: 0.7032 (t0) REVERT: B 133 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7279 (ttmm) REVERT: B 145 ASP cc_start: 0.7745 (p0) cc_final: 0.7351 (p0) REVERT: B 304 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7959 (mp) REVERT: B 341 MET cc_start: 0.5970 (mmt) cc_final: 0.5594 (mmt) REVERT: C 191 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7372 (mm-30) REVERT: C 216 ARG cc_start: 0.6502 (mmm160) cc_final: 0.5918 (mmm160) REVERT: C 225 ILE cc_start: 0.4576 (OUTLIER) cc_final: 0.3882 (mm) REVERT: D 121 GLU cc_start: 0.6773 (mp0) cc_final: 0.6550 (mp0) REVERT: D 140 GLN cc_start: 0.6528 (mp10) cc_final: 0.5392 (mp10) REVERT: D 145 ASP cc_start: 0.5119 (p0) cc_final: 0.4803 (p0) REVERT: D 180 ASP cc_start: 0.7513 (t70) cc_final: 0.6560 (t0) REVERT: D 233 SER cc_start: 0.7571 (m) cc_final: 0.7147 (m) REVERT: E 54 ARG cc_start: 0.6930 (ptt90) cc_final: 0.6617 (ptt90) REVERT: E 88 GLU cc_start: 0.5487 (pp20) cc_final: 0.5175 (pp20) REVERT: E 181 TYR cc_start: 0.7623 (m-80) cc_final: 0.7213 (m-80) outliers start: 69 outliers final: 63 residues processed: 377 average time/residue: 0.1066 time to fit residues: 61.6001 Evaluate side-chains 395 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 318 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 140 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.205086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.165128 restraints weight = 20095.141| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.90 r_work: 0.3429 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16494 Z= 0.166 Angle : 0.574 8.590 22367 Z= 0.303 Chirality : 0.044 0.180 2544 Planarity : 0.004 0.060 2796 Dihedral : 4.291 21.484 2164 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.91 % Allowed : 20.21 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.05 (0.20), residues: 1939 helix: 2.25 (0.16), residues: 960 sheet: 0.43 (0.29), residues: 361 loop : -1.74 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.032 0.001 TYR B 236 PHE 0.018 0.001 PHE E 147 TRP 0.008 0.001 TRP H 119 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00389 (16492) covalent geometry : angle 0.57387 (22363) SS BOND : bond 0.00281 ( 2) SS BOND : angle 1.10593 ( 4) hydrogen bonds : bond 0.05517 ( 970) hydrogen bonds : angle 4.51906 ( 2850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 327 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7518 (ttm110) cc_final: 0.7135 (ttp-110) REVERT: A 87 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6989 (mm) REVERT: A 120 HIS cc_start: 0.6707 (m170) cc_final: 0.6386 (m170) REVERT: A 232 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8163 (mm) REVERT: B 30 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 89 ASP cc_start: 0.7482 (m-30) cc_final: 0.7108 (m-30) REVERT: B 116 ASP cc_start: 0.7668 (t0) cc_final: 0.7020 (t0) REVERT: B 145 ASP cc_start: 0.7708 (p0) cc_final: 0.7311 (p0) REVERT: B 291 MET cc_start: 0.8228 (tpp) cc_final: 0.7680 (mmt) REVERT: B 304 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 341 MET cc_start: 0.5993 (mmt) cc_final: 0.5648 (mmt) REVERT: C 191 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7380 (mm-30) REVERT: C 216 ARG cc_start: 0.6481 (mmm160) cc_final: 0.5974 (mmm160) REVERT: C 267 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7556 (t) REVERT: D 121 GLU cc_start: 0.6913 (mp0) cc_final: 0.6683 (mp0) REVERT: D 140 GLN cc_start: 0.6548 (mp10) cc_final: 0.5380 (mp10) REVERT: D 145 ASP cc_start: 0.5109 (p0) cc_final: 0.4785 (p0) REVERT: D 180 ASP cc_start: 0.7505 (t70) cc_final: 0.6576 (t0) REVERT: D 228 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8235 (mp) REVERT: D 233 SER cc_start: 0.7508 (m) cc_final: 0.7068 (m) REVERT: E 10 LYS cc_start: 0.6373 (pttp) cc_final: 0.5837 (ptpt) REVERT: E 54 ARG cc_start: 0.6933 (ptt90) cc_final: 0.6533 (ptt90) REVERT: E 88 GLU cc_start: 0.5462 (pp20) cc_final: 0.5131 (pp20) REVERT: E 181 TYR cc_start: 0.7599 (m-80) cc_final: 0.7219 (m-80) outliers start: 71 outliers final: 60 residues processed: 368 average time/residue: 0.1008 time to fit residues: 57.0644 Evaluate side-chains 388 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 322 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.0010 chunk 155 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.204963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.164380 restraints weight = 20144.369| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.82 r_work: 0.3417 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16494 Z= 0.170 Angle : 0.587 8.648 22367 Z= 0.309 Chirality : 0.044 0.198 2544 Planarity : 0.005 0.062 2796 Dihedral : 4.293 21.629 2164 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.96 % Allowed : 20.26 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.05 (0.20), residues: 1939 helix: 2.22 (0.16), residues: 960 sheet: 0.46 (0.29), residues: 359 loop : -1.71 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.032 0.001 TYR B 236 PHE 0.019 0.001 PHE E 147 TRP 0.007 0.001 TRP H 119 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00402 (16492) covalent geometry : angle 0.58642 (22363) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.14853 ( 4) hydrogen bonds : bond 0.05519 ( 970) hydrogen bonds : angle 4.51612 ( 2850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 326 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7198 (ttp-110) REVERT: A 87 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6998 (mm) REVERT: A 120 HIS cc_start: 0.6721 (m170) cc_final: 0.6395 (m170) REVERT: A 232 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 291 MET cc_start: 0.6984 (mmp) cc_final: 0.6694 (mmp) REVERT: B 30 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: B 89 ASP cc_start: 0.7513 (m-30) cc_final: 0.7148 (m-30) REVERT: B 116 ASP cc_start: 0.7689 (t0) cc_final: 0.7044 (t0) REVERT: B 145 ASP cc_start: 0.7737 (p0) cc_final: 0.7340 (p0) REVERT: B 304 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 341 MET cc_start: 0.5981 (mmt) cc_final: 0.5609 (mmt) REVERT: C 175 ASP cc_start: 0.6243 (m-30) cc_final: 0.5891 (m-30) REVERT: C 191 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7396 (mm-30) REVERT: C 216 ARG cc_start: 0.6485 (mmm160) cc_final: 0.5991 (mmm160) REVERT: C 225 ILE cc_start: 0.4588 (OUTLIER) cc_final: 0.3807 (mm) REVERT: C 267 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7459 (t) REVERT: D 121 GLU cc_start: 0.6950 (mp0) cc_final: 0.6657 (mp0) REVERT: D 140 GLN cc_start: 0.6594 (mp10) cc_final: 0.5419 (mp10) REVERT: D 145 ASP cc_start: 0.5182 (p0) cc_final: 0.4855 (p0) REVERT: D 180 ASP cc_start: 0.7510 (t70) cc_final: 0.6583 (t0) REVERT: D 228 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8248 (mp) REVERT: D 233 SER cc_start: 0.7376 (m) cc_final: 0.6950 (m) REVERT: E 10 LYS cc_start: 0.6346 (pttp) cc_final: 0.5806 (ptpt) REVERT: E 54 ARG cc_start: 0.6918 (ptt90) cc_final: 0.6543 (ptt90) REVERT: E 88 GLU cc_start: 0.5507 (pp20) cc_final: 0.5184 (pp20) REVERT: E 181 TYR cc_start: 0.7630 (m-80) cc_final: 0.7249 (m-80) outliers start: 72 outliers final: 58 residues processed: 370 average time/residue: 0.1090 time to fit residues: 62.3481 Evaluate side-chains 387 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 34 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.204648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.163814 restraints weight = 20076.015| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.78 r_work: 0.3412 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16494 Z= 0.178 Angle : 0.595 8.988 22367 Z= 0.313 Chirality : 0.045 0.189 2544 Planarity : 0.005 0.062 2796 Dihedral : 4.305 21.850 2164 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.74 % Allowed : 20.43 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 aren not related in a simple way. whole: 1.03 (0.20), residues: 1939 helix: 2.21 (0.16), residues: 960 sheet: 0.46 (0.29), residues: 359 loop : -1.72 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.032 0.002 TYR E 279 PHE 0.018 0.002 PHE E 147 TRP 0.007 0.001 TRP D 226 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00424 (16492) covalent geometry : angle 0.59521 (22363) SS BOND : bond 0.00346 ( 2) SS BOND : angle 1.17197 ( 4) hydrogen bonds : bond 0.05568 ( 970) hydrogen bonds : angle 4.53825 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4047.83 seconds wall clock time: 70 minutes 11.64 seconds (4211.64 seconds total)