Starting phenix.real_space_refine on Mon Jun 16 15:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmh_41389/06_2025/8tmh_41389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmh_41389/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmh_41389/06_2025/8tmh_41389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmh_41389/06_2025/8tmh_41389.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmh_41389/06_2025/8tmh_41389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmh_41389/06_2025/8tmh_41389.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.43, per 1000 atoms: 0.64 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: 4.20 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.87 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: 5.80 Time building geometry restraints manager: 5.02 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.430 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (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 TRP 0.032 0.001 TRP E 325 HIS 0.004 0.001 HIS B 120 PHE 0.019 0.001 PHE A 268 TYR 0.018 0.001 TYR D 279 ARG 0.009 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.16648 ( 1066) hydrogen bonds : angle 6.16792 ( 3132) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.95533 ( 8) covalent geometry : bond 0.00280 (18160) covalent geometry : angle 0.54021 (24631) *********************** 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 : 2.008 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: 0.2908 time to fit residues: 205.7357 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 : 1.942 ------------------------------------------------------------------------------- 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 179 optimal weight: 10.0000 chunk 160 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.0270 chunk 123 optimal weight: 0.0870 chunk 192 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 209 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.192057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3418 r_free = 0.3418 target = 0.138213 restraints weight = 20302.340| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.26 r_work: 0.3183 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18164 Z= 0.142 Angle : 0.556 7.062 24639 Z= 0.297 Chirality : 0.043 0.179 2791 Planarity : 0.004 0.048 3081 Dihedral : 4.236 26.864 2403 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 9.83 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2148 helix: 2.87 (0.16), residues: 981 sheet: 1.10 (0.25), residues: 443 loop : -0.99 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 325 HIS 0.003 0.001 HIS B 120 PHE 0.023 0.001 PHE E 27 TYR 0.021 0.001 TYR C 105 ARG 0.005 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 1066) hydrogen bonds : angle 4.74108 ( 3132) SS BOND : bond 0.00335 ( 4) SS BOND : angle 1.50507 ( 8) covalent geometry : bond 0.00307 (18160) covalent geometry : angle 0.55521 (24631) *********************** 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 486 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 455 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7632 (tmm160) cc_final: 0.6918 (ttm170) REVERT: A 205 LYS cc_start: 0.8051 (tppt) cc_final: 0.7568 (tptp) REVERT: A 279 TYR cc_start: 0.7006 (t80) cc_final: 0.6612 (t80) REVERT: A 341 MET cc_start: 0.7781 (tpt) cc_final: 0.7443 (tpt) REVERT: B 225 ILE cc_start: 0.8754 (tp) cc_final: 0.8497 (pt) REVERT: B 291 MET cc_start: 0.6671 (mmt) cc_final: 0.5376 (mtt) REVERT: B 318 MET cc_start: 0.3096 (ttt) cc_final: 0.2666 (ttt) REVERT: C 190 ASP cc_start: 0.8177 (m-30) cc_final: 0.7925 (m-30) REVERT: D 5 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7281 (ttp-170) REVERT: D 133 LYS cc_start: 0.8382 (ptpt) cc_final: 0.7821 (mmtp) REVERT: D 179 ASP cc_start: 0.8390 (m-30) cc_final: 0.8050 (m-30) REVERT: D 200 LEU cc_start: 0.8249 (mt) cc_final: 0.7795 (mt) REVERT: D 289 GLU cc_start: 0.7953 (tp30) cc_final: 0.7672 (tp30) REVERT: D 291 MET cc_start: 0.6735 (ttm) cc_final: 0.6387 (ttt) REVERT: E 116 ASP cc_start: 0.7443 (t0) cc_final: 0.7231 (t0) REVERT: E 180 ASP cc_start: 0.7854 (t0) cc_final: 0.7648 (t0) REVERT: E 188 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7728 (mp) REVERT: E 192 ILE cc_start: 0.7736 (mt) cc_final: 0.7481 (mt) REVERT: E 252 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6459 (ptt180) REVERT: E 256 ASP cc_start: 0.7893 (m-30) cc_final: 0.7455 (m-30) outliers start: 31 outliers final: 23 residues processed: 468 average time/residue: 0.2994 time to fit residues: 208.5225 Evaluate side-chains 447 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 423 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 293 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 7 SER 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 180 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 188 ILE 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 155 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 133 optimal weight: 0.3980 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 90 GLN B 157 ASN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.189544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.149890 restraints weight = 20143.353| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.09 r_work: 0.3051 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18164 Z= 0.156 Angle : 0.546 7.137 24639 Z= 0.292 Chirality : 0.042 0.171 2791 Planarity : 0.004 0.047 3081 Dihedral : 4.224 18.333 2401 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.06 % Allowed : 12.89 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2148 helix: 2.85 (0.16), residues: 983 sheet: 0.95 (0.25), residues: 440 loop : -1.03 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 325 HIS 0.003 0.001 HIS D 257 PHE 0.024 0.001 PHE E 27 TYR 0.022 0.001 TYR C 105 ARG 0.007 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 1066) hydrogen bonds : angle 4.50676 ( 3132) SS BOND : bond 0.00296 ( 4) SS BOND : angle 1.52859 ( 8) covalent geometry : bond 0.00355 (18160) covalent geometry : angle 0.54550 (24631) *********************** 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 481 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 440 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 83 TYR cc_start: 0.8586 (m-80) cc_final: 0.8366 (m-80) REVERT: A 54 ARG cc_start: 0.7653 (tmm160) cc_final: 0.6993 (ttm170) REVERT: A 89 ASP cc_start: 0.7896 (m-30) cc_final: 0.7470 (m-30) REVERT: A 279 TYR cc_start: 0.7019 (t80) cc_final: 0.6742 (t80) REVERT: A 341 MET cc_start: 0.7840 (tpt) cc_final: 0.7438 (tpt) REVERT: B 202 ARG cc_start: 0.6872 (ptt-90) cc_final: 0.6520 (ptt-90) REVERT: B 291 MET cc_start: 0.6747 (mmt) cc_final: 0.5748 (mtt) REVERT: B 318 MET cc_start: 0.3341 (ttt) cc_final: 0.2730 (ttt) REVERT: C 190 ASP cc_start: 0.8167 (m-30) cc_final: 0.7956 (m-30) REVERT: D 133 LYS cc_start: 0.8364 (ptpt) cc_final: 0.7798 (mmtp) REVERT: D 179 ASP cc_start: 0.8393 (m-30) cc_final: 0.8045 (m-30) REVERT: D 200 LEU cc_start: 0.8221 (mt) cc_final: 0.7760 (mt) REVERT: D 204 GLU cc_start: 0.7259 (mp0) cc_final: 0.7018 (mp0) REVERT: D 289 GLU cc_start: 0.7862 (tp30) cc_final: 0.7584 (tp30) REVERT: D 291 MET cc_start: 0.6786 (ttm) cc_final: 0.6387 (ttt) REVERT: E 98 LYS cc_start: 0.8208 (pttp) cc_final: 0.7839 (pptt) REVERT: E 116 ASP cc_start: 0.7343 (t0) cc_final: 0.7049 (t0) REVERT: E 133 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7216 (mttp) REVERT: E 180 ASP cc_start: 0.7837 (t0) cc_final: 0.7590 (t0) REVERT: E 188 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7636 (mp) REVERT: E 192 ILE cc_start: 0.7727 (mt) cc_final: 0.7454 (mt) REVERT: E 252 ARG cc_start: 0.6867 (ttp-170) cc_final: 0.6238 (ptt180) REVERT: E 256 ASP cc_start: 0.7941 (m-30) cc_final: 0.7497 (m-30) REVERT: E 265 VAL cc_start: 0.8188 (t) cc_final: 0.7958 (m) outliers start: 41 outliers final: 36 residues processed: 455 average time/residue: 0.3048 time to fit residues: 205.8021 Evaluate side-chains 456 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 419 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 154 ILE 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 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 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 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 121 GLU 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 E residue 18 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 91 optimal weight: 0.0030 chunk 74 optimal weight: 0.0060 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5606 ------------------------------------------------------------------------------- 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 E 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.189568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.149813 restraints weight = 20300.608| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.16 r_work: 0.3086 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18164 Z= 0.146 Angle : 0.531 7.095 24639 Z= 0.284 Chirality : 0.042 0.177 2791 Planarity : 0.004 0.047 3081 Dihedral : 4.197 18.655 2401 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.71 % Allowed : 14.34 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.18), residues: 2148 helix: 2.88 (0.16), residues: 984 sheet: 1.00 (0.25), residues: 434 loop : -1.05 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 325 HIS 0.003 0.001 HIS D 68 PHE 0.014 0.001 PHE A 147 TYR 0.021 0.001 TYR C 105 ARG 0.004 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 1066) hydrogen bonds : angle 4.37529 ( 3132) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.31579 ( 8) covalent geometry : bond 0.00330 (18160) covalent geometry : angle 0.53102 (24631) *********************** 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 479 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 425 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 83 TYR cc_start: 0.8618 (m-80) cc_final: 0.8362 (m-80) REVERT: A 54 ARG cc_start: 0.7663 (tmm160) cc_final: 0.6947 (ttm170) REVERT: A 89 ASP cc_start: 0.7992 (m-30) cc_final: 0.7535 (m-30) REVERT: A 205 LYS cc_start: 0.8013 (tppt) cc_final: 0.7440 (tptp) REVERT: A 341 MET cc_start: 0.7864 (tpt) cc_final: 0.7453 (tpt) REVERT: B 202 ARG cc_start: 0.6876 (ptt-90) cc_final: 0.6615 (ptt-90) REVERT: B 225 ILE cc_start: 0.8757 (tp) cc_final: 0.8519 (pt) REVERT: B 291 MET cc_start: 0.6709 (mmt) cc_final: 0.5972 (mtt) REVERT: B 318 MET cc_start: 0.3517 (ttt) cc_final: 0.2951 (ttt) REVERT: C 138 MET cc_start: 0.7687 (mtp) cc_final: 0.7453 (mtt) REVERT: D 5 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7779 (ttp-170) REVERT: D 133 LYS cc_start: 0.8375 (ptpt) cc_final: 0.7839 (mmtp) REVERT: D 179 ASP cc_start: 0.8394 (m-30) cc_final: 0.8052 (m-30) REVERT: D 200 LEU cc_start: 0.8218 (mt) cc_final: 0.7742 (mt) REVERT: D 289 GLU cc_start: 0.7987 (tp30) cc_final: 0.7687 (tp30) REVERT: D 291 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6769 (ttt) REVERT: E 83 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: E 116 ASP cc_start: 0.7392 (t0) cc_final: 0.7132 (t0) REVERT: E 133 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7240 (mttp) REVERT: E 180 ASP cc_start: 0.7868 (t0) cc_final: 0.7531 (t0) REVERT: E 188 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7780 (mp) REVERT: E 192 ILE cc_start: 0.7900 (mt) cc_final: 0.7692 (mt) REVERT: E 252 ARG cc_start: 0.6848 (ttp-170) cc_final: 0.6227 (ptt180) REVERT: E 256 ASP cc_start: 0.7999 (m-30) cc_final: 0.7567 (m-30) REVERT: E 265 VAL cc_start: 0.8272 (t) cc_final: 0.8035 (m) outliers start: 54 outliers final: 40 residues processed: 447 average time/residue: 0.2951 time to fit residues: 200.5386 Evaluate side-chains 461 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 418 time to evaluate : 1.865 ------------------------------------------------------------------------------- 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 6 THR 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 F residue 68 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 154 ILE 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 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 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 39 PHE 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 184 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 83 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 122 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN E 74 GLN E 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.192045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.152951 restraints weight = 20242.790| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.23 r_work: 0.3046 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 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: 0.8045 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18164 Z= 0.149 Angle : 0.532 8.147 24639 Z= 0.283 Chirality : 0.042 0.173 2791 Planarity : 0.004 0.049 3081 Dihedral : 4.198 19.150 2401 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.01 % Allowed : 15.50 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2148 helix: 2.88 (0.16), residues: 985 sheet: 0.97 (0.24), residues: 436 loop : -1.06 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 325 HIS 0.003 0.001 HIS D 68 PHE 0.014 0.001 PHE B 42 TYR 0.022 0.001 TYR C 105 ARG 0.004 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 1066) hydrogen bonds : angle 4.30924 ( 3132) SS BOND : bond 0.00252 ( 4) SS BOND : angle 1.32640 ( 8) covalent geometry : bond 0.00338 (18160) covalent geometry : angle 0.53109 (24631) *********************** 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 486 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 426 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7339 (pt0) cc_final: 0.6933 (pp30) REVERT: G 3 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8406 (mm) REVERT: F 83 TYR cc_start: 0.8596 (m-80) cc_final: 0.8297 (m-80) REVERT: A 30 GLU cc_start: 0.7236 (tt0) cc_final: 0.6765 (tt0) REVERT: A 54 ARG cc_start: 0.7667 (tmm160) cc_final: 0.6939 (ttm170) REVERT: A 89 ASP cc_start: 0.7924 (m-30) cc_final: 0.7497 (m-30) REVERT: A 205 LYS cc_start: 0.7956 (tppt) cc_final: 0.7364 (tptp) REVERT: A 279 TYR cc_start: 0.6906 (t80) cc_final: 0.6607 (t80) REVERT: A 341 MET cc_start: 0.7892 (tpt) cc_final: 0.7474 (tpt) REVERT: B 198 GLU cc_start: 0.7562 (tp30) cc_final: 0.7330 (tp30) REVERT: B 225 ILE cc_start: 0.8715 (tp) cc_final: 0.8425 (pt) REVERT: B 291 MET cc_start: 0.6804 (mmt) cc_final: 0.6221 (mtt) REVERT: B 318 MET cc_start: 0.3834 (ttt) cc_final: 0.3457 (ttt) REVERT: C 152 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6438 (mt-10) REVERT: D 5 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7432 (ttp-170) REVERT: D 133 LYS cc_start: 0.8365 (ptpt) cc_final: 0.7784 (mmtp) REVERT: D 179 ASP cc_start: 0.8411 (m-30) cc_final: 0.8070 (m-30) REVERT: D 200 LEU cc_start: 0.8206 (mt) cc_final: 0.7836 (mt) REVERT: D 289 GLU cc_start: 0.7905 (tp30) cc_final: 0.7587 (tp30) REVERT: E 116 ASP cc_start: 0.7363 (t0) cc_final: 0.7134 (t0) REVERT: E 133 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7221 (mttp) REVERT: E 180 ASP cc_start: 0.7863 (t0) cc_final: 0.7551 (t0) REVERT: E 188 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7695 (mp) REVERT: E 192 ILE cc_start: 0.7818 (mt) cc_final: 0.7604 (mt) REVERT: E 252 ARG cc_start: 0.6818 (ttp-170) cc_final: 0.6175 (ptt180) REVERT: E 256 ASP cc_start: 0.8065 (m-30) cc_final: 0.7603 (m-30) REVERT: E 265 VAL cc_start: 0.8226 (t) cc_final: 0.7982 (m) outliers start: 60 outliers final: 45 residues processed: 453 average time/residue: 0.2913 time to fit residues: 197.4604 Evaluate side-chains 464 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 417 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 7 SER 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 121 GLU 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 41 GLU 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 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 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.189374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.149670 restraints weight = 20091.185| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.19 r_work: 0.3008 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18164 Z= 0.208 Angle : 0.593 7.863 24639 Z= 0.313 Chirality : 0.044 0.175 2791 Planarity : 0.005 0.054 3081 Dihedral : 4.380 20.402 2401 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.01 % Allowed : 15.60 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2148 helix: 2.68 (0.16), residues: 987 sheet: 0.84 (0.24), residues: 456 loop : -1.16 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 325 HIS 0.006 0.001 HIS D 68 PHE 0.018 0.001 PHE B 42 TYR 0.024 0.002 TYR C 105 ARG 0.006 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.05616 ( 1066) hydrogen bonds : angle 4.42517 ( 3132) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.64059 ( 8) covalent geometry : bond 0.00494 (18160) covalent geometry : angle 0.59245 (24631) *********************** 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 500 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 420 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7502 (pttm) cc_final: 0.6984 (ptmm) REVERT: G 3 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8549 (mm) REVERT: F 80 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8057 (t0) REVERT: F 85 GLN cc_start: 0.8488 (tp40) cc_final: 0.8120 (tp40) REVERT: A 38 GLU cc_start: 0.7302 (tp30) cc_final: 0.7064 (tp30) REVERT: A 54 ARG cc_start: 0.7647 (tmm160) cc_final: 0.6994 (ttm170) REVERT: A 89 ASP cc_start: 0.7911 (m-30) cc_final: 0.7450 (m-30) REVERT: A 205 LYS cc_start: 0.7912 (tppt) cc_final: 0.7329 (tptp) REVERT: A 250 TYR cc_start: 0.8663 (m-80) cc_final: 0.8294 (m-80) REVERT: A 279 TYR cc_start: 0.6811 (t80) cc_final: 0.6468 (t80) REVERT: A 341 MET cc_start: 0.7909 (tpt) cc_final: 0.7495 (tpt) REVERT: B 180 ASP cc_start: 0.8218 (t70) cc_final: 0.7981 (t0) REVERT: B 202 ARG cc_start: 0.6978 (ptt-90) cc_final: 0.6776 (ptt-90) REVERT: B 291 MET cc_start: 0.6925 (mmt) cc_final: 0.6587 (mtt) REVERT: B 318 MET cc_start: 0.3782 (ttt) cc_final: 0.3411 (ttt) REVERT: C 189 ASP cc_start: 0.8973 (t0) cc_final: 0.8759 (t0) REVERT: D 133 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7970 (ptpt) REVERT: D 179 ASP cc_start: 0.8419 (m-30) cc_final: 0.8143 (m-30) REVERT: D 200 LEU cc_start: 0.8345 (mt) cc_final: 0.7989 (mt) REVERT: D 204 GLU cc_start: 0.7305 (mp0) cc_final: 0.7043 (mp0) REVERT: D 252 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7561 (tpp80) REVERT: D 279 TYR cc_start: 0.8565 (t80) cc_final: 0.8167 (t80) REVERT: D 289 GLU cc_start: 0.7918 (tp30) cc_final: 0.7544 (tp30) REVERT: E 79 PHE cc_start: 0.8369 (t80) cc_final: 0.7376 (t80) REVERT: E 116 ASP cc_start: 0.7394 (t0) cc_final: 0.7102 (t0) REVERT: E 133 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7193 (mttp) REVERT: E 180 ASP cc_start: 0.7907 (t0) cc_final: 0.7609 (t0) REVERT: E 188 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7702 (mp) REVERT: E 192 ILE cc_start: 0.7858 (mt) cc_final: 0.7624 (mt) REVERT: E 252 ARG cc_start: 0.6847 (ttp-170) cc_final: 0.6151 (ptt180) REVERT: E 256 ASP cc_start: 0.8062 (m-30) cc_final: 0.7585 (m-30) outliers start: 80 outliers final: 65 residues processed: 462 average time/residue: 0.3374 time to fit residues: 235.2950 Evaluate side-chains 477 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 409 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 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 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 273 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 32 MET 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 207 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR 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 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 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 41 GLU Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 98 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.186865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.137165 restraints weight = 20318.330| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.65 r_work: 0.3162 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18164 Z= 0.189 Angle : 0.577 8.231 24639 Z= 0.305 Chirality : 0.043 0.173 2791 Planarity : 0.005 0.051 3081 Dihedral : 4.392 18.574 2401 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.81 % Allowed : 16.70 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2148 helix: 2.68 (0.16), residues: 987 sheet: 0.78 (0.24), residues: 455 loop : -1.15 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 226 HIS 0.005 0.001 HIS D 68 PHE 0.016 0.001 PHE B 42 TYR 0.023 0.002 TYR C 105 ARG 0.005 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 1066) hydrogen bonds : angle 4.38946 ( 3132) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.45831 ( 8) covalent geometry : bond 0.00445 (18160) covalent geometry : angle 0.57612 (24631) *********************** 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 497 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 421 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7565 (pttm) cc_final: 0.7048 (ptmm) REVERT: G 3 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8497 (mm) REVERT: F 80 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8016 (t0) REVERT: F 85 GLN cc_start: 0.8491 (tp40) cc_final: 0.8080 (tp40) REVERT: A 30 GLU cc_start: 0.7184 (tt0) cc_final: 0.6706 (tt0) REVERT: A 54 ARG cc_start: 0.7645 (tmm160) cc_final: 0.7022 (ttm170) REVERT: A 89 ASP cc_start: 0.7851 (m-30) cc_final: 0.7383 (m-30) REVERT: A 205 LYS cc_start: 0.7863 (tppt) cc_final: 0.7276 (tptp) REVERT: A 250 TYR cc_start: 0.8628 (m-80) cc_final: 0.8247 (m-80) REVERT: A 279 TYR cc_start: 0.6773 (t80) cc_final: 0.6437 (t80) REVERT: A 341 MET cc_start: 0.7919 (tpt) cc_final: 0.7494 (tpt) REVERT: B 180 ASP cc_start: 0.8191 (t70) cc_final: 0.7954 (t0) REVERT: B 202 ARG cc_start: 0.6980 (ptt-90) cc_final: 0.6743 (ptt-90) REVERT: B 225 ILE cc_start: 0.8689 (tp) cc_final: 0.8453 (pt) REVERT: B 318 MET cc_start: 0.3774 (ttt) cc_final: 0.3390 (ttt) REVERT: D 5 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7793 (ttp-170) REVERT: D 133 LYS cc_start: 0.8394 (ptpt) cc_final: 0.7931 (ptpt) REVERT: D 179 ASP cc_start: 0.8358 (m-30) cc_final: 0.8098 (m-30) REVERT: D 200 LEU cc_start: 0.8343 (mt) cc_final: 0.7982 (mt) REVERT: D 204 GLU cc_start: 0.7275 (mp0) cc_final: 0.6995 (mp0) REVERT: D 252 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7456 (tpp80) REVERT: D 279 TYR cc_start: 0.8482 (t80) cc_final: 0.8103 (t80) REVERT: D 289 GLU cc_start: 0.7822 (tp30) cc_final: 0.7448 (tp30) REVERT: D 291 MET cc_start: 0.6719 (ttm) cc_final: 0.6339 (ttt) REVERT: E 79 PHE cc_start: 0.8396 (t80) cc_final: 0.7408 (t80) REVERT: E 116 ASP cc_start: 0.7406 (t0) cc_final: 0.7124 (t0) REVERT: E 133 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7235 (mttp) REVERT: E 180 ASP cc_start: 0.7793 (t0) cc_final: 0.7478 (t0) REVERT: E 188 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7667 (mp) REVERT: E 190 ASP cc_start: 0.6544 (m-30) cc_final: 0.6286 (m-30) REVERT: E 192 ILE cc_start: 0.7802 (mt) cc_final: 0.7570 (mt) REVERT: E 252 ARG cc_start: 0.6829 (ttp-170) cc_final: 0.6116 (ptt180) REVERT: E 256 ASP cc_start: 0.8045 (m-30) cc_final: 0.7558 (m-30) outliers start: 76 outliers final: 61 residues processed: 457 average time/residue: 0.2967 time to fit residues: 203.0267 Evaluate side-chains 478 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 414 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 92 GLU 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 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 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 A residue 275 LEU Chi-restraints excluded: chain B residue 32 MET 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 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 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 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 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 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 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 99 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 114 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.188291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3392 r_free = 0.3392 target = 0.135928 restraints weight = 20358.835| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.28 r_work: 0.3165 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18164 Z= 0.141 Angle : 0.542 8.483 24639 Z= 0.287 Chirality : 0.042 0.170 2791 Planarity : 0.004 0.050 3081 Dihedral : 4.271 17.762 2401 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.56 % Allowed : 17.30 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2148 helix: 2.80 (0.16), residues: 987 sheet: 0.85 (0.24), residues: 445 loop : -1.07 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 226 HIS 0.003 0.001 HIS B 120 PHE 0.011 0.001 PHE B 42 TYR 0.021 0.001 TYR C 19 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 1066) hydrogen bonds : angle 4.26595 ( 3132) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.16105 ( 8) covalent geometry : bond 0.00317 (18160) covalent geometry : angle 0.54140 (24631) *********************** 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 500 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 429 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7497 (pttm) cc_final: 0.6985 (ptmm) REVERT: G 3 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 30 GLU cc_start: 0.7172 (tt0) cc_final: 0.6701 (tt0) REVERT: A 33 ASN cc_start: 0.7278 (t0) cc_final: 0.6899 (t0) REVERT: A 54 ARG cc_start: 0.7630 (tmm160) cc_final: 0.7019 (ttm170) REVERT: A 89 ASP cc_start: 0.7934 (m-30) cc_final: 0.7606 (m-30) REVERT: A 148 ASP cc_start: 0.8577 (m-30) cc_final: 0.8316 (m-30) REVERT: A 205 LYS cc_start: 0.7837 (tppt) cc_final: 0.7292 (tptp) REVERT: A 250 TYR cc_start: 0.8619 (m-80) cc_final: 0.8233 (m-80) REVERT: A 279 TYR cc_start: 0.6809 (t80) cc_final: 0.6522 (t80) REVERT: A 341 MET cc_start: 0.7977 (tpt) cc_final: 0.7561 (tpt) REVERT: B 318 MET cc_start: 0.3816 (ttt) cc_final: 0.3472 (ttt) REVERT: C 210 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6892 (mmm160) REVERT: D 5 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7733 (ttp-170) REVERT: D 133 LYS cc_start: 0.8420 (ptpt) cc_final: 0.7806 (mmtp) REVERT: D 179 ASP cc_start: 0.8360 (m-30) cc_final: 0.8081 (m-30) REVERT: D 200 LEU cc_start: 0.8314 (mt) cc_final: 0.7957 (mt) REVERT: D 204 GLU cc_start: 0.7290 (mp0) cc_final: 0.7036 (mp0) REVERT: D 289 GLU cc_start: 0.7916 (tp30) cc_final: 0.7563 (tp30) REVERT: D 318 MET cc_start: 0.3229 (ttt) cc_final: 0.1827 (tpp) REVERT: E 79 PHE cc_start: 0.8390 (t80) cc_final: 0.7421 (t80) REVERT: E 116 ASP cc_start: 0.7412 (t0) cc_final: 0.7129 (t0) REVERT: E 133 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7226 (mttp) REVERT: E 180 ASP cc_start: 0.7799 (t0) cc_final: 0.7496 (t0) REVERT: E 188 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7695 (mp) REVERT: E 190 ASP cc_start: 0.6602 (m-30) cc_final: 0.6337 (m-30) REVERT: E 192 ILE cc_start: 0.7817 (mt) cc_final: 0.7580 (mt) REVERT: E 197 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6268 (tm-30) REVERT: E 252 ARG cc_start: 0.6789 (ttp-170) cc_final: 0.6153 (ptt180) REVERT: E 256 ASP cc_start: 0.8064 (m-30) cc_final: 0.7620 (m-30) outliers start: 71 outliers final: 61 residues processed: 460 average time/residue: 0.2964 time to fit residues: 203.2993 Evaluate side-chains 483 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 420 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 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 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 106 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 A residue 275 LEU Chi-restraints excluded: chain B residue 32 MET 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 341 MET 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 D residue 7 SER Chi-restraints excluded: chain D residue 25 GLU 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 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 148 ASP 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 182 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.187664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.139675 restraints weight = 20344.758| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.70 r_work: 0.3199 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18164 Z= 0.169 Angle : 0.567 8.577 24639 Z= 0.299 Chirality : 0.043 0.202 2791 Planarity : 0.004 0.051 3081 Dihedral : 4.323 17.902 2401 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.31 % Allowed : 18.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.18), residues: 2148 helix: 2.73 (0.16), residues: 986 sheet: 0.81 (0.24), residues: 457 loop : -1.12 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 226 HIS 0.005 0.001 HIS D 68 PHE 0.015 0.001 PHE B 42 TYR 0.024 0.001 TYR D 279 ARG 0.005 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 1066) hydrogen bonds : angle 4.29624 ( 3132) SS BOND : bond 0.00238 ( 4) SS BOND : angle 1.40453 ( 8) covalent geometry : bond 0.00394 (18160) covalent geometry : angle 0.56654 (24631) *********************** 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 482 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 416 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7509 (pttm) cc_final: 0.7001 (ptmm) REVERT: G 3 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8503 (mm) REVERT: F 80 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8031 (t0) REVERT: F 85 GLN cc_start: 0.8450 (tp40) cc_final: 0.8160 (tp40) REVERT: A 30 GLU cc_start: 0.7178 (tt0) cc_final: 0.6714 (tt0) REVERT: A 33 ASN cc_start: 0.7286 (t0) cc_final: 0.6931 (t0) REVERT: A 54 ARG cc_start: 0.7651 (tmm160) cc_final: 0.7049 (ttm170) REVERT: A 89 ASP cc_start: 0.7939 (m-30) cc_final: 0.7606 (m-30) REVERT: A 250 TYR cc_start: 0.8641 (m-80) cc_final: 0.8264 (m-80) REVERT: A 291 MET cc_start: 0.7074 (tpt) cc_final: 0.6773 (ttt) REVERT: A 341 MET cc_start: 0.7889 (tpt) cc_final: 0.7458 (tpt) REVERT: B 155 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8109 (ttm170) REVERT: B 180 ASP cc_start: 0.8161 (t70) cc_final: 0.7941 (t0) REVERT: B 318 MET cc_start: 0.3791 (ttt) cc_final: 0.3415 (ttt) REVERT: C 210 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6892 (mmm160) REVERT: C 291 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6327 (mtm) REVERT: D 5 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.7755 (ttp-170) REVERT: D 133 LYS cc_start: 0.8429 (ptpt) cc_final: 0.7942 (ptpt) REVERT: D 179 ASP cc_start: 0.8383 (m-30) cc_final: 0.8095 (m-30) REVERT: D 204 GLU cc_start: 0.7294 (mp0) cc_final: 0.7012 (mp0) REVERT: D 289 GLU cc_start: 0.7877 (tp30) cc_final: 0.7507 (tp30) REVERT: D 291 MET cc_start: 0.6802 (ttm) cc_final: 0.6228 (ttt) REVERT: D 318 MET cc_start: 0.3274 (ttt) cc_final: 0.1921 (tpp) REVERT: E 79 PHE cc_start: 0.8343 (t80) cc_final: 0.7366 (t80) REVERT: E 116 ASP cc_start: 0.7460 (t0) cc_final: 0.7221 (t0) REVERT: E 121 GLU cc_start: 0.7398 (pt0) cc_final: 0.6636 (pm20) REVERT: E 133 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7238 (mttp) REVERT: E 180 ASP cc_start: 0.7767 (t0) cc_final: 0.7470 (t0) REVERT: E 188 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7710 (mp) REVERT: E 190 ASP cc_start: 0.6585 (m-30) cc_final: 0.6317 (m-30) REVERT: E 192 ILE cc_start: 0.7836 (mt) cc_final: 0.7586 (mt) REVERT: E 252 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6166 (ptt180) REVERT: E 256 ASP cc_start: 0.8038 (m-30) cc_final: 0.7604 (m-30) REVERT: E 341 MET cc_start: 0.7910 (mmt) cc_final: 0.7698 (mmt) outliers start: 66 outliers final: 59 residues processed: 448 average time/residue: 0.3089 time to fit residues: 206.1969 Evaluate side-chains 473 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 410 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 92 GLU 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 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 106 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 273 SER Chi-restraints excluded: chain A residue 275 LEU 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 157 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 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 C residue 291 MET Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 GLU 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 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 183 VAL 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 180 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 171 optimal weight: 0.8980 chunk 211 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.191867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.152152 restraints weight = 19945.350| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.17 r_work: 0.3030 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- 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 = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18164 Z= 0.167 Angle : 0.570 8.900 24639 Z= 0.300 Chirality : 0.043 0.213 2791 Planarity : 0.004 0.049 3081 Dihedral : 4.331 18.054 2401 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.31 % Allowed : 17.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2148 helix: 2.71 (0.16), residues: 986 sheet: 0.79 (0.24), residues: 456 loop : -1.10 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 226 HIS 0.004 0.001 HIS D 68 PHE 0.018 0.001 PHE C 306 TYR 0.038 0.001 TYR D 279 ARG 0.006 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 1066) hydrogen bonds : angle 4.28914 ( 3132) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.35249 ( 8) covalent geometry : bond 0.00391 (18160) covalent geometry : angle 0.56978 (24631) ********************** 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 486 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 1.806 Fit side-chains revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7479 (pttm) cc_final: 0.6990 (ptmm) REVERT: G 3 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8473 (mm) REVERT: F 80 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8003 (t0) REVERT: F 85 GLN cc_start: 0.8449 (tp40) cc_final: 0.8145 (tp40) REVERT: A 30 GLU cc_start: 0.7116 (tt0) cc_final: 0.6634 (tt0) REVERT: A 33 ASN cc_start: 0.7228 (t0) cc_final: 0.6874 (t0) REVERT: A 54 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7016 (ttm170) REVERT: A 89 ASP cc_start: 0.7918 (m-30) cc_final: 0.7588 (m-30) REVERT: A 250 TYR cc_start: 0.8624 (m-80) cc_final: 0.8243 (m-80) REVERT: A 341 MET cc_start: 0.7910 (tpt) cc_final: 0.7469 (tpt) REVERT: B 155 ARG cc_start: 0.8228 (ttm170) cc_final: 0.8015 (ttm170) REVERT: B 318 MET cc_start: 0.3807 (ttt) cc_final: 0.3445 (ttt) REVERT: C 210 ARG cc_start: 0.7173 (mmm-85) cc_final: 0.6845 (mmm160) REVERT: C 291 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6273 (mtm) REVERT: D 5 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7728 (ttp-170) REVERT: D 133 LYS cc_start: 0.8425 (ptpt) cc_final: 0.7940 (ptpt) REVERT: D 179 ASP cc_start: 0.8389 (m-30) cc_final: 0.8109 (m-30) REVERT: D 200 LEU cc_start: 0.8314 (mt) cc_final: 0.7945 (mt) REVERT: D 204 GLU cc_start: 0.7300 (mp0) cc_final: 0.6992 (mp0) REVERT: D 289 GLU cc_start: 0.7855 (tp30) cc_final: 0.7476 (tp30) REVERT: D 291 MET cc_start: 0.6799 (ttm) cc_final: 0.6198 (ttt) REVERT: D 318 MET cc_start: 0.3266 (ttt) cc_final: 0.1898 (tpp) REVERT: E 32 MET cc_start: 0.7665 (ttm) cc_final: 0.7405 (ttp) REVERT: E 79 PHE cc_start: 0.8317 (t80) cc_final: 0.7326 (t80) REVERT: E 116 ASP cc_start: 0.7437 (t0) cc_final: 0.7207 (t0) REVERT: E 133 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7154 (mttp) REVERT: E 180 ASP cc_start: 0.7769 (t0) cc_final: 0.7474 (t0) REVERT: E 188 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7642 (mp) REVERT: E 190 ASP cc_start: 0.6530 (m-30) cc_final: 0.6263 (m-30) REVERT: E 192 ILE cc_start: 0.7789 (mt) cc_final: 0.7551 (mt) REVERT: E 217 ASN cc_start: 0.8487 (m-40) cc_final: 0.8231 (m110) REVERT: E 252 ARG cc_start: 0.6785 (ttp-170) cc_final: 0.6114 (ptt180) REVERT: E 256 ASP cc_start: 0.8042 (m-30) cc_final: 0.7580 (m-30) outliers start: 66 outliers final: 59 residues processed: 453 average time/residue: 0.2946 time to fit residues: 199.4347 Evaluate side-chains 476 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 413 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 92 GLU 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 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 106 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 273 SER Chi-restraints excluded: chain A residue 275 LEU 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 236 TYR 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 236 TYR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 GLU 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 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 183 VAL 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 151 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 38 optimal weight: 0.0870 chunk 48 optimal weight: 0.0570 chunk 186 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 112 optimal weight: 0.4980 chunk 122 optimal weight: 0.1980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.189894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.149134 restraints weight = 20293.515| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.33 r_work: 0.3095 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18164 Z= 0.130 Angle : 0.551 8.830 24639 Z= 0.289 Chirality : 0.042 0.193 2791 Planarity : 0.004 0.050 3081 Dihedral : 4.213 18.052 2401 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.11 % Allowed : 18.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2148 helix: 2.85 (0.16), residues: 986 sheet: 0.90 (0.24), residues: 444 loop : -1.05 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 226 HIS 0.003 0.001 HIS B 120 PHE 0.015 0.001 PHE C 306 TYR 0.033 0.001 TYR D 279 ARG 0.006 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 1066) hydrogen bonds : angle 4.16172 ( 3132) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.02950 ( 8) covalent geometry : bond 0.00286 (18160) covalent geometry : angle 0.55110 (24631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12181.36 seconds wall clock time: 209 minutes 40.78 seconds (12580.78 seconds total)