Starting phenix.real_space_refine on Sun Aug 24 09:34:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmh_41389/08_2025/8tmh_41389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmh_41389/08_2025/8tmh_41389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tmh_41389/08_2025/8tmh_41389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmh_41389/08_2025/8tmh_41389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tmh_41389/08_2025/8tmh_41389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmh_41389/08_2025/8tmh_41389.map" } resolution = 3.1 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= 0.042 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 1577 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 65 5.16 5 C 11504 2.51 5 N 2894 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s 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: 17756 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2899 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2812 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain: "D" 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: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "C" 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: 3.78, per 1000 atoms: 0.21 Number of scatterers: 17756 At special positions: 0 Unit cell: (129.228, 133.5, 159.132, 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 65 16.00 Mg 2 11.99 O 3291 8.00 N 2894 7.00 C 11504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 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: 1.32 Conformation dependent library (CDL) restraints added in 705.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 17 sheets defined 47.9% alpha, 21.8% 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 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.741A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.842A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.839A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.778A pdb=" N SER A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Proline residue: A 52 - end of helix No H-bonds generated for 'chain 'A' and resid 46 through 54' Processing helix chain 'A' and resid 69 through 81 removed outlier: 4.139A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.900A pdb=" N ARG A 162 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.679A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 4.007A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.804A pdb=" N ASP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 282 removed outlier: 3.692A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 307 removed outlier: 4.294A pdb=" N VAL A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.561A pdb=" N PHE B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 202 Processing helix chain 'B' and resid 204 through 237 Proline residue: B 227 - end of helix removed outlier: 3.678A pdb=" N GLU B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 312 removed outlier: 3.589A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 325 through 347 Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.901A pdb=" N VAL C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 51' Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.968A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.503A pdb=" N LYS C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 removed outlier: 3.959A pdb=" N VAL C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 3.617A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 282 removed outlier: 4.186A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 313 removed outlier: 3.921A pdb=" N ILE C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 325 through 348 removed outlier: 3.732A pdb=" N VAL C 329 " --> pdb=" O TRP C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.536A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.541A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.603A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 239 removed outlier: 4.103A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.828A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 311 Proline residue: D 303 - end of helix removed outlier: 3.807A pdb=" N TYR D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'E' and resid 69 through 81 removed outlier: 4.153A 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 165 through 202 removed outlier: 3.506A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 237 removed outlier: 4.245A pdb=" N GLN E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 247 through 311 removed outlier: 4.193A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 326 through 348 removed outlier: 4.092A pdb=" N LYS E 348 " --> pdb=" O TYR E 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.616A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR H 118 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR H 103 " --> pdb=" O MET H 116 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET H 116 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR H 105 " --> pdb=" O ASN H 114 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN H 114 " --> pdb=" O TYR H 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.616A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.556A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.556A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.506A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.517A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AB2, first strand: chain 'F' and resid 61 through 63 removed outlier: 6.641A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER F 36 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG F 101 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 61 through 63 removed outlier: 6.641A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER F 36 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.691A pdb=" N ILE A 29 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 123 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 114 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 44 removed outlier: 4.415A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 116 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.630A pdb=" N LEU C 110 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 44 removed outlier: 3.702A pdb=" N GLU D 123 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.510A pdb=" N VAL E 31 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS E 98 " --> pdb=" O VAL E 109 " (cutoff:3.500A) 1094 hydrogen bonds defined for protein. 3132 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: 2.58 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5601 1.34 - 1.46: 3873 1.46 - 1.58: 8569 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 18160 Sorted by residual: bond pdb=" CB PRO L 9 " pdb=" CG PRO L 9 " ideal model delta sigma weight residual 1.506 1.568 -0.062 3.90e-02 6.57e+02 2.52e+00 bond pdb=" CG1 ILE E 188 " pdb=" CD1 ILE E 188 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CA ASN A 314 " pdb=" CB ASN A 314 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.53e-02 4.27e+03 1.52e+00 bond pdb=" CB ASN A 314 " pdb=" CG ASN A 314 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CG1 ILE B 297 " pdb=" CD1 ILE B 297 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.33e-01 ... (remaining 18155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24191 1.68 - 3.36: 353 3.36 - 5.04: 70 5.04 - 6.72: 12 6.72 - 8.40: 5 Bond angle restraints: 24631 Sorted by residual: angle pdb=" C VAL D 290 " pdb=" N MET D 291 " pdb=" CA MET D 291 " ideal model delta sigma weight residual 122.06 114.59 7.47 1.86e+00 2.89e-01 1.61e+01 angle pdb=" C LEU C 235 " pdb=" N TYR C 236 " pdb=" CA TYR C 236 " ideal model delta sigma weight residual 122.53 115.35 7.18 1.92e+00 2.71e-01 1.40e+01 angle pdb=" N VAL C 283 " pdb=" CA VAL C 283 " pdb=" C VAL C 283 " ideal model delta sigma weight residual 113.71 110.27 3.44 9.50e-01 1.11e+00 1.31e+01 angle pdb=" C MET A 313 " pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 123.47 128.36 -4.89 1.53e+00 4.27e-01 1.02e+01 angle pdb=" N ILE A 307 " pdb=" CA ILE A 307 " pdb=" C ILE A 307 " ideal model delta sigma weight residual 110.05 106.80 3.25 1.09e+00 8.42e-01 8.91e+00 ... (remaining 24626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9685 17.92 - 35.84: 979 35.84 - 53.76: 162 53.76 - 71.68: 34 71.68 - 89.60: 20 Dihedral angle restraints: 10880 sinusoidal: 4470 harmonic: 6410 Sorted by residual: dihedral pdb=" CA LEU D 119 " pdb=" C LEU D 119 " pdb=" N HIS D 120 " pdb=" CA HIS D 120 " ideal model delta harmonic sigma weight residual 180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 61.75 31.25 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CA ARG C 24 " pdb=" C ARG C 24 " pdb=" N GLU C 25 " pdb=" CA GLU C 25 " ideal model delta harmonic sigma weight residual -180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1883 0.035 - 0.071: 631 0.071 - 0.106: 209 0.106 - 0.141: 62 0.141 - 0.177: 6 Chirality restraints: 2791 Sorted by residual: chirality pdb=" CB ILE E 67 " pdb=" CA ILE E 67 " pdb=" CG1 ILE E 67 " pdb=" CG2 ILE E 67 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CG LEU E 184 " pdb=" CB LEU E 184 " pdb=" CD1 LEU E 184 " pdb=" CD2 LEU E 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA ASP A 180 " pdb=" N ASP A 180 " pdb=" C ASP A 180 " pdb=" CB ASP A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 2788 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 51 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO E 52 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 52 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 52 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 325 " 0.011 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP E 325 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP E 325 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 325 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 325 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 325 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 325 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 325 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 325 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 325 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 240 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO E 241 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 241 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 241 " 0.023 5.00e-02 4.00e+02 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 281 2.68 - 3.24: 16927 3.24 - 3.79: 27587 3.79 - 4.35: 37264 4.35 - 4.90: 61937 Nonbonded interactions: 143996 Sorted by model distance: nonbonded pdb=" O LYS E 111 " pdb=" OH TYR E 181 " model vdw 2.129 3.040 nonbonded pdb=" OH TYR H 35 " pdb=" OD1 ASP D 71 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASN D 288 " pdb=" OG1 THR E 287 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP C 26 " pdb=" N PHE C 27 " model vdw 2.197 3.120 nonbonded pdb=" OE1 GLN L 91 " pdb=" OG SER L 93 " model vdw 2.236 3.040 ... (remaining 143991 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' selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } ncs_group { reference = chain 'F' selection = (chain 'H' and resid 4 through 126) } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.160 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.003 0.062 18164 Z= 0.129 Angle : 0.540 8.401 24639 Z= 0.286 Chirality : 0.041 0.177 2791 Planarity : 0.004 0.047 3081 Dihedral : 14.687 89.598 6734 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.10 % Allowed : 0.55 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.93 (0.19), residues: 2148 helix: 2.92 (0.16), residues: 970 sheet: 1.05 (0.25), residues: 456 loop : -0.94 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 222 TYR 0.018 0.001 TYR D 279 PHE 0.019 0.001 PHE A 268 TRP 0.032 0.001 TRP E 325 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00280 (18160) covalent geometry : angle 0.54021 (24631) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.95533 ( 8) hydrogen bonds : bond 0.16648 ( 1066) hydrogen bonds : angle 6.16792 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 3 ILE cc_start: 0.8230 (mm) cc_final: 0.7951 (mm) REVERT: A 279 TYR cc_start: 0.6305 (t80) cc_final: 0.6080 (t80) REVERT: B 26 ASP cc_start: 0.7158 (m-30) cc_final: 0.6929 (m-30) REVERT: B 202 ARG cc_start: 0.6979 (ptt-90) cc_final: 0.6700 (ptt-90) REVERT: B 291 MET cc_start: 0.5660 (mmt) cc_final: 0.5035 (mtt) REVERT: D 133 LYS cc_start: 0.8023 (ptpt) cc_final: 0.7664 (mmmt) REVERT: D 179 ASP cc_start: 0.7874 (m-30) cc_final: 0.7521 (m-30) REVERT: D 200 LEU cc_start: 0.8422 (mt) cc_final: 0.8041 (mt) REVERT: D 289 GLU cc_start: 0.7146 (tp30) cc_final: 0.6899 (tp30) REVERT: D 318 MET cc_start: 0.5983 (ttp) cc_final: 0.4076 (mtm) REVERT: E 192 ILE cc_start: 0.8098 (mt) cc_final: 0.7877 (mt) outliers start: 2 outliers final: 1 residues processed: 468 average time/residue: 0.1170 time to fit residues: 83.3926 Evaluate side-chains 427 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 90 GLN B 209 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.186717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3348 r_free = 0.3348 target = 0.132522 restraints weight = 20145.510| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.19 r_work: 0.3119 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18164 Z= 0.247 Angle : 0.633 7.203 24639 Z= 0.338 Chirality : 0.046 0.179 2791 Planarity : 0.005 0.061 3081 Dihedral : 4.487 26.884 2403 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 1.91 % Allowed : 10.28 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.61 (0.18), residues: 2148 helix: 2.59 (0.16), residues: 983 sheet: 0.87 (0.25), residues: 460 loop : -1.08 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 67 TYR 0.021 0.002 TYR C 105 PHE 0.023 0.002 PHE E 27 TRP 0.021 0.001 TRP E 325 HIS 0.007 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00584 (18160) covalent geometry : angle 0.63211 (24631) SS BOND : bond 0.00366 ( 4) SS BOND : angle 2.30305 ( 8) hydrogen bonds : bond 0.06201 ( 1066) hydrogen bonds : angle 4.86083 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 433 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7168 (ttm-80) REVERT: G 25 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: A 205 LYS cc_start: 0.8038 (tppt) cc_final: 0.7505 (tptp) REVERT: A 279 TYR cc_start: 0.7017 (t80) cc_final: 0.6609 (t80) REVERT: A 341 MET cc_start: 0.7814 (tpt) cc_final: 0.7476 (tpt) REVERT: B 291 MET cc_start: 0.6752 (mmt) cc_final: 0.5533 (mtt) REVERT: B 318 MET cc_start: 0.3082 (ttt) cc_final: 0.2663 (ttt) REVERT: C 112 MET cc_start: 0.8879 (mtp) cc_final: 0.8654 (mtp) REVERT: C 126 GLN cc_start: 0.8400 (tt0) cc_final: 0.8141 (tt0) REVERT: D 38 GLU cc_start: 0.7687 (pt0) cc_final: 0.7091 (pt0) REVERT: D 133 LYS cc_start: 0.8403 (ptpt) cc_final: 0.7971 (ptpt) REVERT: D 179 ASP cc_start: 0.8504 (m-30) cc_final: 0.8184 (m-30) REVERT: D 200 LEU cc_start: 0.8389 (mt) cc_final: 0.8120 (mt) REVERT: D 252 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7705 (tpp80) REVERT: D 289 GLU cc_start: 0.7930 (tp30) cc_final: 0.7670 (tp30) REVERT: E 79 PHE cc_start: 0.8352 (t80) cc_final: 0.7465 (t80) REVERT: E 116 ASP cc_start: 0.7473 (t0) cc_final: 0.7230 (t0) REVERT: E 180 ASP cc_start: 0.7932 (t0) cc_final: 0.7706 (t0) REVERT: E 188 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7810 (mp) REVERT: E 192 ILE cc_start: 0.7772 (mt) cc_final: 0.7523 (mt) REVERT: E 256 ASP cc_start: 0.8081 (m-30) cc_final: 0.7635 (m-30) REVERT: E 265 VAL cc_start: 0.8239 (t) cc_final: 0.8022 (m) outliers start: 38 outliers final: 32 residues processed: 451 average time/residue: 0.1554 time to fit residues: 103.9933 Evaluate side-chains 444 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 411 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 125 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 195 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.192752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152997 restraints weight = 20121.542| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.17 r_work: 0.3048 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18164 Z= 0.147 Angle : 0.547 7.152 24639 Z= 0.292 Chirality : 0.042 0.172 2791 Planarity : 0.004 0.047 3081 Dihedral : 4.310 17.774 2401 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.41 % Allowed : 13.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.72 (0.18), residues: 2148 helix: 2.75 (0.16), residues: 985 sheet: 0.85 (0.25), residues: 449 loop : -1.05 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 69 TYR 0.022 0.001 TYR C 105 PHE 0.014 0.001 PHE A 147 TRP 0.015 0.001 TRP E 325 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00325 (18160) covalent geometry : angle 0.54612 (24631) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.42389 ( 8) hydrogen bonds : bond 0.05376 ( 1066) hydrogen bonds : angle 4.54515 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 445 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 3 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8364 (mm) REVERT: G 28 GLN cc_start: 0.8316 (tt0) cc_final: 0.8111 (tt0) REVERT: A 54 ARG cc_start: 0.7624 (tmm160) cc_final: 0.6963 (ttm170) REVERT: A 89 ASP cc_start: 0.7900 (m-30) cc_final: 0.7453 (m-30) REVERT: A 279 TYR cc_start: 0.7036 (t80) cc_final: 0.6724 (t80) REVERT: A 341 MET cc_start: 0.7812 (tpt) cc_final: 0.7404 (tpt) REVERT: B 180 ASP cc_start: 0.8184 (t70) cc_final: 0.7952 (t0) REVERT: B 202 ARG cc_start: 0.6925 (ptt-90) cc_final: 0.6573 (ptt-90) REVERT: B 225 ILE cc_start: 0.8716 (tp) cc_final: 0.8478 (pt) REVERT: B 291 MET cc_start: 0.6819 (mmt) cc_final: 0.5871 (mtt) REVERT: B 318 MET cc_start: 0.3309 (ttt) cc_final: 0.2736 (ttt) REVERT: C 112 MET cc_start: 0.8839 (mtp) cc_final: 0.8595 (mtp) REVERT: C 180 ASP cc_start: 0.8064 (t0) cc_final: 0.7730 (t0) REVERT: C 190 ASP cc_start: 0.8231 (m-30) cc_final: 0.8019 (m-30) REVERT: D 133 LYS cc_start: 0.8350 (ptpt) cc_final: 0.7792 (mmtp) REVERT: D 179 ASP cc_start: 0.8405 (m-30) cc_final: 0.8073 (m-30) REVERT: D 200 LEU cc_start: 0.8224 (mt) cc_final: 0.7896 (mt) REVERT: D 289 GLU cc_start: 0.7847 (tp30) cc_final: 0.7545 (tp30) REVERT: E 54 ARG cc_start: 0.7239 (ttp-170) cc_final: 0.6868 (ttp-170) REVERT: E 79 PHE cc_start: 0.8346 (t80) cc_final: 0.7353 (t80) REVERT: E 116 ASP cc_start: 0.7412 (t0) cc_final: 0.7184 (t0) REVERT: E 180 ASP cc_start: 0.7876 (t0) cc_final: 0.7544 (t0) REVERT: E 188 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7635 (mp) REVERT: E 192 ILE cc_start: 0.7771 (mt) cc_final: 0.7508 (mt) REVERT: E 252 ARG cc_start: 0.6912 (ttp-170) cc_final: 0.6250 (ptt180) REVERT: E 256 ASP cc_start: 0.8021 (m-30) cc_final: 0.7553 (m-30) REVERT: E 265 VAL cc_start: 0.8183 (t) cc_final: 0.7955 (m) REVERT: E 291 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5692 (mmp) outliers start: 48 outliers final: 37 residues processed: 463 average time/residue: 0.1536 time to fit residues: 106.0913 Evaluate side-chains 466 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 426 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 82 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 0.0070 chunk 173 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN B 157 ASN C 63 ASN E 74 GLN E 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.193572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.153342 restraints weight = 20158.861| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.82 r_work: 0.3093 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18164 Z= 0.124 Angle : 0.519 7.642 24639 Z= 0.277 Chirality : 0.041 0.172 2791 Planarity : 0.004 0.047 3081 Dihedral : 4.190 19.069 2401 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.91 % Allowed : 14.99 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.86 (0.18), residues: 2148 helix: 2.90 (0.16), residues: 985 sheet: 1.01 (0.25), residues: 433 loop : -1.06 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 69 TYR 0.021 0.001 TYR C 105 PHE 0.015 0.001 PHE B 39 TRP 0.013 0.001 TRP E 325 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00261 (18160) covalent geometry : angle 0.51873 (24631) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.14826 ( 8) hydrogen bonds : bond 0.04835 ( 1066) hydrogen bonds : angle 4.32196 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 442 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7346 (pt0) cc_final: 0.6962 (pp30) REVERT: L 5 MET cc_start: 0.8536 (mtp) cc_final: 0.8117 (mtp) REVERT: G 3 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 33 ASN cc_start: 0.7445 (t0) cc_final: 0.7031 (t0) REVERT: A 54 ARG cc_start: 0.7622 (tmm160) cc_final: 0.6916 (ttm170) REVERT: A 89 ASP cc_start: 0.7873 (m-30) cc_final: 0.7435 (m-30) REVERT: A 205 LYS cc_start: 0.7972 (tppt) cc_final: 0.7422 (tptp) REVERT: A 341 MET cc_start: 0.7898 (tpt) cc_final: 0.7489 (tpt) REVERT: B 202 ARG cc_start: 0.6828 (ptt-90) cc_final: 0.6555 (ptt-90) REVERT: B 276 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 318 MET cc_start: 0.3452 (ttt) cc_final: 0.2955 (ttt) REVERT: C 112 MET cc_start: 0.8775 (mtp) cc_final: 0.8545 (mtp) REVERT: C 180 ASP cc_start: 0.8043 (t0) cc_final: 0.7751 (t0) REVERT: D 133 LYS cc_start: 0.8328 (ptpt) cc_final: 0.7918 (mttt) REVERT: D 179 ASP cc_start: 0.8292 (m-30) cc_final: 0.7938 (m-30) REVERT: D 200 LEU cc_start: 0.8262 (mt) cc_final: 0.7777 (mt) REVERT: D 204 GLU cc_start: 0.7227 (mp0) cc_final: 0.7021 (mp0) REVERT: D 289 GLU cc_start: 0.7878 (tp30) cc_final: 0.7544 (tp30) REVERT: E 116 ASP cc_start: 0.7347 (t0) cc_final: 0.7063 (t0) REVERT: E 133 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7204 (mttp) REVERT: E 180 ASP cc_start: 0.7778 (t0) cc_final: 0.7475 (t0) REVERT: E 188 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7598 (mp) REVERT: E 192 ILE cc_start: 0.7740 (mt) cc_final: 0.7536 (mt) REVERT: E 252 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6238 (ptt180) REVERT: E 256 ASP cc_start: 0.7910 (m-30) cc_final: 0.7436 (m-30) REVERT: E 265 VAL cc_start: 0.8166 (t) cc_final: 0.7916 (m) outliers start: 58 outliers final: 38 residues processed: 464 average time/residue: 0.1484 time to fit residues: 103.7443 Evaluate side-chains 464 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 423 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 199 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN E 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.188651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.148132 restraints weight = 20088.691| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.29 r_work: 0.3025 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18164 Z= 0.232 Angle : 0.600 7.287 24639 Z= 0.319 Chirality : 0.045 0.178 2791 Planarity : 0.005 0.056 3081 Dihedral : 4.424 20.286 2401 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.56 % Allowed : 15.25 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.58 (0.18), residues: 2148 helix: 2.64 (0.16), residues: 987 sheet: 0.79 (0.24), residues: 456 loop : -1.18 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 67 TYR 0.022 0.002 TYR C 105 PHE 0.014 0.002 PHE A 301 TRP 0.013 0.001 TRP E 325 HIS 0.006 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00556 (18160) covalent geometry : angle 0.59928 (24631) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.80046 ( 8) hydrogen bonds : bond 0.05735 ( 1066) hydrogen bonds : angle 4.48785 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 405 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: G 3 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8616 (mm) REVERT: F 85 GLN cc_start: 0.8557 (tp40) cc_final: 0.8186 (tp40) REVERT: A 54 ARG cc_start: 0.7689 (tmm160) cc_final: 0.6990 (ttm170) REVERT: A 89 ASP cc_start: 0.8008 (m-30) cc_final: 0.7622 (m-30) REVERT: A 205 LYS cc_start: 0.7975 (tppt) cc_final: 0.7384 (tptp) REVERT: A 279 TYR cc_start: 0.6948 (t80) cc_final: 0.6595 (t80) REVERT: A 341 MET cc_start: 0.7891 (tpt) cc_final: 0.7480 (tpt) REVERT: B 180 ASP cc_start: 0.8247 (t70) cc_final: 0.8010 (t0) REVERT: B 197 GLU cc_start: 0.8374 (tp30) cc_final: 0.8174 (tp30) REVERT: B 291 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6173 (mmt) REVERT: B 318 MET cc_start: 0.3540 (ttt) cc_final: 0.2996 (ttt) REVERT: C 112 MET cc_start: 0.8810 (mtp) cc_final: 0.8536 (mtp) REVERT: C 180 ASP cc_start: 0.8235 (t0) cc_final: 0.7919 (t0) REVERT: D 133 LYS cc_start: 0.8449 (ptpt) cc_final: 0.7991 (ptpt) REVERT: D 179 ASP cc_start: 0.8466 (m-30) cc_final: 0.8181 (m-30) REVERT: D 252 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7601 (tpp80) REVERT: D 289 GLU cc_start: 0.7990 (tp30) cc_final: 0.7662 (tp30) REVERT: E 116 ASP cc_start: 0.7476 (t0) cc_final: 0.7198 (t0) REVERT: E 180 ASP cc_start: 0.7957 (t0) cc_final: 0.7646 (t0) REVERT: E 188 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7800 (mp) REVERT: E 192 ILE cc_start: 0.7884 (mt) cc_final: 0.7588 (mt) REVERT: E 252 ARG cc_start: 0.6916 (ttp-170) cc_final: 0.6240 (ptt180) REVERT: E 256 ASP cc_start: 0.8165 (m-30) cc_final: 0.7697 (m-30) outliers start: 71 outliers final: 59 residues processed: 441 average time/residue: 0.1524 time to fit residues: 100.5568 Evaluate side-chains 457 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 395 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 59 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.188112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3364 r_free = 0.3364 target = 0.133742 restraints weight = 20276.140| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.18 r_work: 0.3145 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18164 Z= 0.152 Angle : 0.549 8.132 24639 Z= 0.291 Chirality : 0.042 0.172 2791 Planarity : 0.004 0.050 3081 Dihedral : 4.317 20.335 2401 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.36 % Allowed : 16.45 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.71 (0.18), residues: 2148 helix: 2.78 (0.16), residues: 986 sheet: 0.79 (0.24), residues: 455 loop : -1.10 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 222 TYR 0.021 0.001 TYR C 105 PHE 0.012 0.001 PHE A 301 TRP 0.011 0.001 TRP E 325 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00346 (18160) covalent geometry : angle 0.54895 (24631) SS BOND : bond 0.00231 ( 4) SS BOND : angle 1.26775 ( 8) hydrogen bonds : bond 0.05188 ( 1066) hydrogen bonds : angle 4.34050 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 423 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: L 5 MET cc_start: 0.8615 (mtp) cc_final: 0.8189 (mtp) REVERT: G 3 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (mm) REVERT: F 85 GLN cc_start: 0.8516 (tp40) cc_final: 0.8092 (tp40) REVERT: A 33 ASN cc_start: 0.7417 (t0) cc_final: 0.7047 (t0) REVERT: A 54 ARG cc_start: 0.7627 (tmm160) cc_final: 0.6961 (ttm170) REVERT: A 89 ASP cc_start: 0.7934 (m-30) cc_final: 0.7498 (m-30) REVERT: A 205 LYS cc_start: 0.7951 (tppt) cc_final: 0.7409 (tptp) REVERT: A 250 TYR cc_start: 0.8654 (m-80) cc_final: 0.8294 (m-80) REVERT: A 279 TYR cc_start: 0.6939 (t80) cc_final: 0.6591 (t80) REVERT: A 341 MET cc_start: 0.7960 (tpt) cc_final: 0.7545 (tpt) REVERT: B 180 ASP cc_start: 0.8261 (t70) cc_final: 0.7934 (t0) REVERT: B 202 ARG cc_start: 0.7055 (ptt-90) cc_final: 0.6784 (ptt-90) REVERT: B 291 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5803 (mmt) REVERT: B 318 MET cc_start: 0.3842 (ttt) cc_final: 0.3435 (ttt) REVERT: C 112 MET cc_start: 0.8827 (mtp) cc_final: 0.8555 (mtp) REVERT: C 180 ASP cc_start: 0.8213 (t0) cc_final: 0.7896 (t0) REVERT: D 133 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7819 (mmtp) REVERT: D 179 ASP cc_start: 0.8372 (m-30) cc_final: 0.8103 (m-30) REVERT: D 200 LEU cc_start: 0.8335 (mt) cc_final: 0.7979 (mt) REVERT: D 289 GLU cc_start: 0.7977 (tp30) cc_final: 0.7629 (tp30) REVERT: E 116 ASP cc_start: 0.7421 (t0) cc_final: 0.7110 (t0) REVERT: E 133 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7226 (mttp) REVERT: E 180 ASP cc_start: 0.7887 (t0) cc_final: 0.7591 (t0) REVERT: E 188 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7693 (mp) REVERT: E 190 ASP cc_start: 0.6615 (m-30) cc_final: 0.6357 (m-30) REVERT: E 192 ILE cc_start: 0.7838 (mt) cc_final: 0.7619 (mt) REVERT: E 252 ARG cc_start: 0.6869 (ttp-170) cc_final: 0.6221 (ptt180) REVERT: E 256 ASP cc_start: 0.8120 (m-30) cc_final: 0.7658 (m-30) REVERT: E 265 VAL cc_start: 0.8230 (t) cc_final: 0.7970 (m) outliers start: 67 outliers final: 49 residues processed: 456 average time/residue: 0.1497 time to fit residues: 102.6444 Evaluate side-chains 466 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 414 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 8 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.186295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.133188 restraints weight = 20135.431| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.08 r_work: 0.3094 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 18164 Z= 0.262 Angle : 0.636 7.925 24639 Z= 0.335 Chirality : 0.045 0.179 2791 Planarity : 0.005 0.063 3081 Dihedral : 4.577 20.561 2401 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 3.76 % Allowed : 16.80 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.40 (0.18), residues: 2148 helix: 2.50 (0.16), residues: 987 sheet: 0.68 (0.24), residues: 456 loop : -1.26 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 67 TYR 0.021 0.002 TYR C 105 PHE 0.016 0.002 PHE A 301 TRP 0.013 0.001 TRP C 226 HIS 0.007 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00631 (18160) covalent geometry : angle 0.63515 (24631) SS BOND : bond 0.00339 ( 4) SS BOND : angle 1.83141 ( 8) hydrogen bonds : bond 0.06053 ( 1066) hydrogen bonds : angle 4.54266 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 411 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7572 (pttm) cc_final: 0.7079 (ptmm) REVERT: F 80 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8093 (t0) REVERT: F 85 GLN cc_start: 0.8557 (tp40) cc_final: 0.8087 (tp40) REVERT: A 54 ARG cc_start: 0.7720 (tmm160) cc_final: 0.7110 (ttm170) REVERT: A 89 ASP cc_start: 0.8017 (m-30) cc_final: 0.7598 (m-30) REVERT: A 148 ASP cc_start: 0.8612 (m-30) cc_final: 0.8355 (m-30) REVERT: A 191 GLU cc_start: 0.8777 (tt0) cc_final: 0.8530 (tt0) REVERT: A 250 TYR cc_start: 0.8745 (m-80) cc_final: 0.8395 (m-80) REVERT: A 279 TYR cc_start: 0.6871 (t80) cc_final: 0.6526 (t80) REVERT: A 341 MET cc_start: 0.7984 (tpt) cc_final: 0.7549 (tpt) REVERT: B 155 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8203 (ttm170) REVERT: B 180 ASP cc_start: 0.8330 (t70) cc_final: 0.8102 (t0) REVERT: B 291 MET cc_start: 0.6329 (mmt) cc_final: 0.5987 (mmt) REVERT: B 318 MET cc_start: 0.3858 (ttt) cc_final: 0.3438 (ttt) REVERT: C 112 MET cc_start: 0.8798 (mtp) cc_final: 0.8507 (mtp) REVERT: C 180 ASP cc_start: 0.8369 (t0) cc_final: 0.8127 (t0) REVERT: C 206 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6026 (tp30) REVERT: D 133 LYS cc_start: 0.8484 (ptpt) cc_final: 0.7971 (ptpt) REVERT: D 179 ASP cc_start: 0.8572 (m-30) cc_final: 0.8311 (m-30) REVERT: D 189 ASP cc_start: 0.8524 (t0) cc_final: 0.8271 (t0) REVERT: D 200 LEU cc_start: 0.8426 (mt) cc_final: 0.8060 (mt) REVERT: D 252 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7678 (tpp80) REVERT: D 289 GLU cc_start: 0.7977 (tp30) cc_final: 0.7624 (tp30) REVERT: E 116 ASP cc_start: 0.7511 (t0) cc_final: 0.7305 (t0) REVERT: E 180 ASP cc_start: 0.7986 (t0) cc_final: 0.7687 (t0) REVERT: E 188 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7794 (mp) REVERT: E 190 ASP cc_start: 0.6621 (m-30) cc_final: 0.6360 (m-30) REVERT: E 192 ILE cc_start: 0.7896 (mt) cc_final: 0.7595 (mt) REVERT: E 217 ASN cc_start: 0.8585 (m-40) cc_final: 0.8357 (m110) REVERT: E 252 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6262 (ptt180) REVERT: E 256 ASP cc_start: 0.8131 (m-30) cc_final: 0.7677 (m-30) outliers start: 75 outliers final: 64 residues processed: 450 average time/residue: 0.1580 time to fit residues: 106.3835 Evaluate side-chains 468 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 402 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 28 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.190022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.141994 restraints weight = 20075.392| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.61 r_work: 0.3213 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18164 Z= 0.165 Angle : 0.572 8.538 24639 Z= 0.302 Chirality : 0.043 0.171 2791 Planarity : 0.005 0.052 3081 Dihedral : 4.432 19.764 2401 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 3.36 % Allowed : 17.90 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.58 (0.18), residues: 2148 helix: 2.68 (0.16), residues: 988 sheet: 0.72 (0.24), residues: 455 loop : -1.20 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 222 TYR 0.020 0.001 TYR C 105 PHE 0.015 0.001 PHE A 301 TRP 0.012 0.001 TRP C 226 HIS 0.007 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00381 (18160) covalent geometry : angle 0.57167 (24631) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.32576 ( 8) hydrogen bonds : bond 0.05432 ( 1066) hydrogen bonds : angle 4.39783 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 412 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7437 (pttm) cc_final: 0.6985 (ptmm) REVERT: L 5 MET cc_start: 0.8534 (mtp) cc_final: 0.8075 (mtp) REVERT: G 3 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8439 (mm) REVERT: F 80 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8039 (t0) REVERT: F 85 GLN cc_start: 0.8554 (tp40) cc_final: 0.8085 (tp40) REVERT: A 33 ASN cc_start: 0.7272 (t0) cc_final: 0.6915 (t0) REVERT: A 54 ARG cc_start: 0.7683 (tmm160) cc_final: 0.7006 (ttm170) REVERT: A 89 ASP cc_start: 0.7802 (m-30) cc_final: 0.7351 (m-30) REVERT: A 148 ASP cc_start: 0.8513 (m-30) cc_final: 0.8253 (m-30) REVERT: A 205 LYS cc_start: 0.7974 (tppt) cc_final: 0.7362 (tptp) REVERT: A 279 TYR cc_start: 0.6625 (t80) cc_final: 0.6311 (t80) REVERT: A 341 MET cc_start: 0.7899 (tpt) cc_final: 0.7452 (tpt) REVERT: B 180 ASP cc_start: 0.8152 (t70) cc_final: 0.7912 (t0) REVERT: B 291 MET cc_start: 0.6453 (mmt) cc_final: 0.6193 (mmt) REVERT: B 318 MET cc_start: 0.3781 (ttt) cc_final: 0.3368 (ttt) REVERT: C 112 MET cc_start: 0.8733 (mtp) cc_final: 0.8451 (mtp) REVERT: C 180 ASP cc_start: 0.8249 (t0) cc_final: 0.7974 (t0) REVERT: D 133 LYS cc_start: 0.8393 (ptpt) cc_final: 0.7936 (ptpt) REVERT: D 179 ASP cc_start: 0.8427 (m-30) cc_final: 0.8146 (m-30) REVERT: D 189 ASP cc_start: 0.8374 (t0) cc_final: 0.8085 (t0) REVERT: D 200 LEU cc_start: 0.8402 (mt) cc_final: 0.8041 (mt) REVERT: D 204 GLU cc_start: 0.7231 (mp0) cc_final: 0.6963 (mp0) REVERT: D 252 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7516 (tpp80) REVERT: D 289 GLU cc_start: 0.7849 (tp30) cc_final: 0.7479 (tp30) REVERT: E 116 ASP cc_start: 0.7467 (t0) cc_final: 0.7246 (t0) REVERT: E 133 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7238 (mttp) REVERT: E 180 ASP cc_start: 0.7846 (t0) cc_final: 0.7552 (t0) REVERT: E 188 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7680 (mp) REVERT: E 190 ASP cc_start: 0.6572 (m-30) cc_final: 0.6274 (m-30) REVERT: E 192 ILE cc_start: 0.7865 (mt) cc_final: 0.7636 (mt) REVERT: E 217 ASN cc_start: 0.8535 (m-40) cc_final: 0.8296 (m110) REVERT: E 252 ARG cc_start: 0.6845 (ttp-170) cc_final: 0.6155 (ptt180) REVERT: E 256 ASP cc_start: 0.8012 (m-30) cc_final: 0.7550 (m-30) outliers start: 67 outliers final: 57 residues processed: 444 average time/residue: 0.1525 time to fit residues: 101.3541 Evaluate side-chains 467 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 407 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 37 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.191851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.139294 restraints weight = 20155.301| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.06 r_work: 0.3164 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18164 Z= 0.136 Angle : 0.549 8.722 24639 Z= 0.289 Chirality : 0.042 0.170 2791 Planarity : 0.004 0.052 3081 Dihedral : 4.298 20.658 2401 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.51 % Allowed : 17.65 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.71 (0.18), residues: 2148 helix: 2.82 (0.16), residues: 985 sheet: 0.78 (0.24), residues: 445 loop : -1.12 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 222 TYR 0.023 0.001 TYR D 279 PHE 0.011 0.001 PHE A 147 TRP 0.011 0.001 TRP C 226 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00303 (18160) covalent geometry : angle 0.54892 (24631) SS BOND : bond 0.00369 ( 4) SS BOND : angle 1.12160 ( 8) hydrogen bonds : bond 0.04944 ( 1066) hydrogen bonds : angle 4.24948 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 418 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7401 (pttm) cc_final: 0.6900 (ptmm) REVERT: L 5 MET cc_start: 0.8595 (mtp) cc_final: 0.8205 (mtp) REVERT: G 3 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8452 (mm) REVERT: F 85 GLN cc_start: 0.8544 (tp40) cc_final: 0.8072 (tp40) REVERT: A 30 GLU cc_start: 0.7169 (tt0) cc_final: 0.6675 (tt0) REVERT: A 33 ASN cc_start: 0.7270 (t0) cc_final: 0.6931 (t0) REVERT: A 54 ARG cc_start: 0.7660 (tmm160) cc_final: 0.7035 (ttm170) REVERT: A 89 ASP cc_start: 0.7864 (m-30) cc_final: 0.7376 (m-30) REVERT: A 148 ASP cc_start: 0.8607 (m-30) cc_final: 0.8364 (m-30) REVERT: A 205 LYS cc_start: 0.7926 (tppt) cc_final: 0.7255 (tptp) REVERT: A 279 TYR cc_start: 0.6847 (t80) cc_final: 0.6532 (t80) REVERT: A 291 MET cc_start: 0.7704 (mmm) cc_final: 0.7475 (mmt) REVERT: A 318 MET cc_start: 0.6270 (tpt) cc_final: 0.3132 (ttm) REVERT: A 341 MET cc_start: 0.7940 (tpt) cc_final: 0.7498 (tpt) REVERT: B 318 MET cc_start: 0.3823 (ttt) cc_final: 0.3451 (ttt) REVERT: C 112 MET cc_start: 0.8862 (mtp) cc_final: 0.8587 (mtp) REVERT: C 202 ARG cc_start: 0.6860 (ptt90) cc_final: 0.6572 (ptt90) REVERT: C 315 PHE cc_start: 0.4398 (OUTLIER) cc_final: 0.4182 (m-10) REVERT: D 133 LYS cc_start: 0.8439 (ptpt) cc_final: 0.7834 (mmtp) REVERT: D 179 ASP cc_start: 0.8356 (m-30) cc_final: 0.8067 (m-30) REVERT: D 204 GLU cc_start: 0.7205 (mp0) cc_final: 0.6908 (mp0) REVERT: D 289 GLU cc_start: 0.7952 (tp30) cc_final: 0.7588 (tp30) REVERT: E 116 ASP cc_start: 0.7471 (t0) cc_final: 0.7227 (t0) REVERT: E 133 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7281 (mttp) REVERT: E 180 ASP cc_start: 0.7784 (t0) cc_final: 0.7492 (t0) REVERT: E 188 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7748 (mp) REVERT: E 190 ASP cc_start: 0.6649 (m-30) cc_final: 0.6386 (m-30) REVERT: E 192 ILE cc_start: 0.7833 (mt) cc_final: 0.7629 (mt) REVERT: E 252 ARG cc_start: 0.6819 (ttp-170) cc_final: 0.6192 (ptt180) REVERT: E 256 ASP cc_start: 0.8130 (m-30) cc_final: 0.7681 (m-30) outliers start: 70 outliers final: 60 residues processed: 453 average time/residue: 0.1474 time to fit residues: 100.0187 Evaluate side-chains 469 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 406 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 192 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 208 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.189372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.136695 restraints weight = 20189.071| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.14 r_work: 0.3153 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18164 Z= 0.155 Angle : 0.568 8.715 24639 Z= 0.298 Chirality : 0.043 0.172 2791 Planarity : 0.004 0.053 3081 Dihedral : 4.316 18.723 2401 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.21 % Allowed : 18.10 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.69 (0.18), residues: 2148 helix: 2.77 (0.16), residues: 987 sheet: 0.79 (0.24), residues: 456 loop : -1.13 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 67 TYR 0.036 0.001 TYR D 279 PHE 0.012 0.001 PHE A 301 TRP 0.012 0.001 TRP C 226 HIS 0.006 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00360 (18160) covalent geometry : angle 0.56780 (24631) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.34640 ( 8) hydrogen bonds : bond 0.05068 ( 1066) hydrogen bonds : angle 4.25742 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 406 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7376 (pttm) cc_final: 0.6875 (ptmm) REVERT: L 5 MET cc_start: 0.8609 (mtp) cc_final: 0.8196 (mtp) REVERT: G 3 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8519 (mm) REVERT: F 85 GLN cc_start: 0.8524 (tp40) cc_final: 0.8040 (tp40) REVERT: A 30 GLU cc_start: 0.7146 (tt0) cc_final: 0.6655 (tt0) REVERT: A 54 ARG cc_start: 0.7654 (tmm160) cc_final: 0.7033 (ttm170) REVERT: A 89 ASP cc_start: 0.7892 (m-30) cc_final: 0.7520 (m-30) REVERT: A 148 ASP cc_start: 0.8603 (m-30) cc_final: 0.8356 (m-30) REVERT: A 205 LYS cc_start: 0.7867 (tppt) cc_final: 0.7203 (tptp) REVERT: A 279 TYR cc_start: 0.6752 (t80) cc_final: 0.6431 (t80) REVERT: A 318 MET cc_start: 0.6219 (tpt) cc_final: 0.3105 (ttm) REVERT: A 341 MET cc_start: 0.7958 (tpt) cc_final: 0.7523 (tpt) REVERT: B 180 ASP cc_start: 0.8184 (t70) cc_final: 0.7952 (t0) REVERT: B 318 MET cc_start: 0.3823 (ttt) cc_final: 0.3467 (ttt) REVERT: C 112 MET cc_start: 0.8822 (mtp) cc_final: 0.8554 (mtp) REVERT: C 180 ASP cc_start: 0.8115 (t0) cc_final: 0.7892 (t0) REVERT: C 202 ARG cc_start: 0.6870 (ptt90) cc_final: 0.6580 (ptt90) REVERT: C 315 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.4193 (m-10) REVERT: D 133 LYS cc_start: 0.8439 (ptpt) cc_final: 0.7827 (mmtp) REVERT: D 179 ASP cc_start: 0.8383 (m-30) cc_final: 0.8011 (m-30) REVERT: D 204 GLU cc_start: 0.7248 (mp0) cc_final: 0.6910 (mp0) REVERT: D 289 GLU cc_start: 0.7985 (tp30) cc_final: 0.7636 (tp30) REVERT: D 291 MET cc_start: 0.6655 (ttm) cc_final: 0.6331 (ttt) REVERT: E 133 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7293 (mttp) REVERT: E 180 ASP cc_start: 0.7788 (t0) cc_final: 0.7494 (t0) REVERT: E 188 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7760 (mp) REVERT: E 190 ASP cc_start: 0.6638 (m-30) cc_final: 0.6406 (m-30) REVERT: E 192 ILE cc_start: 0.7852 (mt) cc_final: 0.7612 (mt) REVERT: E 252 ARG cc_start: 0.6822 (ttp-170) cc_final: 0.6198 (ptt180) REVERT: E 256 ASP cc_start: 0.8115 (m-30) cc_final: 0.7672 (m-30) outliers start: 64 outliers final: 59 residues processed: 438 average time/residue: 0.1467 time to fit residues: 96.5579 Evaluate side-chains 461 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 399 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 2 optimal weight: 0.8980 chunk 192 optimal weight: 0.0970 chunk 208 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.193232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.141199 restraints weight = 20110.842| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.03 r_work: 0.3174 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18164 Z= 0.138 Angle : 0.555 8.869 24639 Z= 0.291 Chirality : 0.042 0.170 2791 Planarity : 0.004 0.052 3081 Dihedral : 4.267 20.348 2401 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.21 % Allowed : 18.51 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.74 (0.18), residues: 2148 helix: 2.82 (0.16), residues: 985 sheet: 0.86 (0.24), residues: 444 loop : -1.13 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 222 TYR 0.033 0.001 TYR D 279 PHE 0.016 0.001 PHE C 306 TRP 0.011 0.001 TRP C 226 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00311 (18160) covalent geometry : angle 0.55487 (24631) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.17652 ( 8) hydrogen bonds : bond 0.04869 ( 1066) hydrogen bonds : angle 4.20107 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6380.61 seconds wall clock time: 109 minutes 38.54 seconds (6578.54 seconds total)