Starting phenix.real_space_refine on Thu Mar 13 22:17:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch6_30369/03_2025/7ch6_30369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch6_30369/03_2025/7ch6_30369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2025/7ch6_30369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2025/7ch6_30369.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2025/7ch6_30369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2025/7ch6_30369_neut.cif" } resolution = 3.4 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 58 5.16 5 C 5934 2.51 5 N 1584 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.63 Number of scatterers: 9260 At special positions: 0 Unit cell: (105.04, 109.2, 112.32, 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 58 16.00 P 6 15.00 O 1678 8.00 N 1584 7.00 C 5934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 57.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 removed outlier: 3.684A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.855A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.804A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.605A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.837A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 138 through 152 removed outlier: 4.935A pdb=" N SER A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 154 through 175 removed outlier: 3.842A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.602A pdb=" N LEU A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 259 removed outlier: 3.544A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 4.914A pdb=" N THR B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.855A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 79 removed outlier: 3.803A pdb=" N SER B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 86 through 96 removed outlier: 3.605A pdb=" N LEU B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 removed outlier: 3.838A pdb=" N VAL B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 138 through 152 removed outlier: 4.934A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.841A pdb=" N VAL B 160 " --> pdb=" O PRO B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 195 through 217 removed outlier: 3.603A pdb=" N LEU B 199 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 259 removed outlier: 3.544A pdb=" N SER B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.992A pdb=" N THR C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 117 through 133 removed outlier: 3.575A pdb=" N SER C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.699A pdb=" N ALA C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.628A pdb=" N ILE C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.903A pdb=" N GLN C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 removed outlier: 3.978A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 78 through 85 removed outlier: 3.991A pdb=" N THR D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 117 through 133 removed outlier: 3.576A pdb=" N SER D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.699A pdb=" N ALA D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.628A pdb=" N ILE D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.902A pdb=" N GLN D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.977A pdb=" N PHE D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'E' and resid 25 through 31 removed outlier: 3.504A pdb=" N TRP E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 31' Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.596A pdb=" N GLN E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 88 removed outlier: 3.658A pdb=" N TYR E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 removed outlier: 3.504A pdb=" N TRP F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 31' Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 51 through 68 removed outlier: 3.598A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 removed outlier: 3.658A pdb=" N TYR F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 32 removed outlier: 5.797A pdb=" N ILE C 27 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 13 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 88 through 90 removed outlier: 7.144A pdb=" N ILE C 166 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL C 201 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE C 168 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 37 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER C 202 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE C 39 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA C 38 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 218 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET C 40 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 27 through 32 removed outlier: 5.797A pdb=" N ILE D 27 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 13 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 88 through 90 removed outlier: 7.143A pdb=" N ILE D 166 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL D 201 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE D 168 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 37 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER D 202 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE D 39 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA D 38 " --> pdb=" O TRP D 216 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU D 218 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET D 40 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AA6, first strand: chain 'E' and resid 42 through 43 removed outlier: 6.786A pdb=" N ILE E 42 " --> pdb=" O GLN E 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 9 Processing sheet with id=AA8, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.785A pdb=" N ILE F 42 " --> pdb=" O GLN F 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 422 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3003 1.34 - 1.46: 1620 1.46 - 1.57: 4695 1.57 - 1.69: 10 1.69 - 1.81: 108 Bond restraints: 9436 Sorted by residual: bond pdb=" N3B ANP C 301 " pdb=" PG ANP C 301 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" O3A ANP C 301 " pdb=" PB ANP C 301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP D 301 " pdb=" PA ANP D 301 " ideal model delta sigma weight residual 1.655 1.602 0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 9431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 12423 1.92 - 3.83: 329 3.83 - 5.75: 70 5.75 - 7.67: 6 7.67 - 9.59: 6 Bond angle restraints: 12834 Sorted by residual: angle pdb=" C ASP C 204 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " ideal model delta sigma weight residual 120.43 124.33 -3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" C ASP D 204 " pdb=" N VAL D 205 " pdb=" CA VAL D 205 " ideal model delta sigma weight residual 120.43 124.33 -3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" C VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta sigma weight residual 113.70 110.36 3.34 9.50e-01 1.11e+00 1.24e+01 angle pdb=" C VAL D 205 " pdb=" CA VAL D 205 " pdb=" CB VAL D 205 " ideal model delta sigma weight residual 113.70 110.40 3.30 9.50e-01 1.11e+00 1.20e+01 angle pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " pdb=" O2G ANP D 301 " ideal model delta sigma weight residual 101.05 110.61 -9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 12829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 5261 23.78 - 47.56: 314 47.56 - 71.34: 78 71.34 - 95.12: 11 95.12 - 118.89: 4 Dihedral angle restraints: 5668 sinusoidal: 2228 harmonic: 3440 Sorted by residual: dihedral pdb=" CA LEU E 95 " pdb=" C LEU E 95 " pdb=" N PRO E 96 " pdb=" CA PRO E 96 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU F 95 " pdb=" C LEU F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA MET B 134 " pdb=" C MET B 134 " pdb=" N MET B 135 " pdb=" CA MET B 135 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.951: 1535 0.951 - 1.902: 0 1.902 - 2.853: 0 2.853 - 3.803: 0 3.803 - 4.754: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C1' ANP C 301 " pdb=" C2' ANP C 301 " pdb=" N9 ANP C 301 " pdb=" O4' ANP C 301 " both_signs ideal model delta sigma weight residual False 2.42 -2.33 4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C3' ANP C 301 " pdb=" C2' ANP C 301 " pdb=" C4' ANP C 301 " pdb=" O3' ANP C 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' ANP D 301 " pdb=" C2' ANP D 301 " pdb=" C4' ANP D 301 " pdb=" O3' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1533 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 95 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO E 96 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 95 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO F 96 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 41 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO B 42 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.021 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 160 2.64 - 3.21: 9166 3.21 - 3.77: 14614 3.77 - 4.34: 20172 4.34 - 4.90: 33320 Nonbonded interactions: 77432 Sorted by model distance: nonbonded pdb=" N3 ANP C 301 " pdb=" O2' ANP C 301 " model vdw 2.077 3.120 nonbonded pdb=" OG SER B 130 " pdb=" OE1 GLN C 57 " model vdw 2.104 3.040 nonbonded pdb=" OG SER A 228 " pdb=" OG SER B 228 " model vdw 2.117 3.040 nonbonded pdb=" OG SER A 131 " pdb=" NH2 ARG D 157 " model vdw 2.117 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 62 " model vdw 2.128 3.040 ... (remaining 77427 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: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.820 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.008 0.165 9436 Z= 0.524 Angle : 0.821 9.587 12834 Z= 0.451 Chirality : 0.130 4.754 1536 Planarity : 0.006 0.118 1606 Dihedral : 16.465 118.895 3456 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 12.88 % Allowed : 11.87 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.20), residues: 1202 helix: -2.92 (0.15), residues: 650 sheet: -0.75 (0.94), residues: 40 loop : -3.21 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 195 HIS 0.004 0.001 HIS D 113 PHE 0.015 0.002 PHE A 162 TYR 0.011 0.002 TYR D 256 ARG 0.005 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 257 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 51 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 70 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 96 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 116 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7888 (mtm) REVERT: A 244 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 247 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 31 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8686 (mt) REVERT: B 70 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 96 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 116 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7382 (mp) REVERT: B 123 MET cc_start: 0.8040 (mtt) cc_final: 0.7769 (mtm) REVERT: B 244 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 247 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (mm) REVERT: C 170 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: C 176 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (p0) REVERT: C 178 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8872 (tt) REVERT: D 170 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: D 249 ASP cc_start: 0.7664 (t0) cc_final: 0.7358 (p0) REVERT: E 63 ASP cc_start: 0.7917 (t70) cc_final: 0.7700 (t70) REVERT: F 21 ASP cc_start: 0.8688 (p0) cc_final: 0.8117 (p0) REVERT: F 89 ASN cc_start: 0.8389 (t0) cc_final: 0.7832 (t0) outliers start: 128 outliers final: 47 residues processed: 356 average time/residue: 0.2645 time to fit residues: 131.3351 Evaluate side-chains 254 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 190 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 50 ASN A 190 GLN B 47 GLN B 50 ASN B 190 GLN C 214 HIS D 175 GLN D 214 HIS E 75 GLN F 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096841 restraints weight = 14136.097| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.84 r_work: 0.3060 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9436 Z= 0.240 Angle : 0.724 9.710 12834 Z= 0.345 Chirality : 0.045 0.156 1536 Planarity : 0.006 0.109 1606 Dihedral : 12.910 93.084 1471 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 9.46 % Allowed : 17.51 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.22), residues: 1202 helix: -1.75 (0.18), residues: 640 sheet: -2.16 (0.61), residues: 78 loop : -2.85 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 7 HIS 0.007 0.001 HIS C 113 PHE 0.013 0.001 PHE C 91 TYR 0.011 0.001 TYR D 81 ARG 0.014 0.001 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 216 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 51 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8754 (t) REVERT: A 56 MET cc_start: 0.8454 (ttm) cc_final: 0.8066 (mtt) REVERT: A 96 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 116 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 120 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8336 (pt) REVERT: A 123 MET cc_start: 0.8470 (mtt) cc_final: 0.8248 (mtm) REVERT: B 31 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 70 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (tt) REVERT: B 96 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8396 (tt) REVERT: B 120 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8240 (pt) REVERT: B 123 MET cc_start: 0.8440 (mtt) cc_final: 0.8204 (mtm) REVERT: B 198 ASP cc_start: 0.8103 (t0) cc_final: 0.7731 (t0) REVERT: C 105 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8015 (m-40) REVERT: C 172 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8014 (p90) REVERT: D 105 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7960 (m-40) REVERT: D 172 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8092 (p90) REVERT: D 249 ASP cc_start: 0.8234 (t0) cc_final: 0.7536 (p0) REVERT: E 89 ASN cc_start: 0.8761 (t0) cc_final: 0.7999 (t0) REVERT: F 89 ASN cc_start: 0.8729 (t0) cc_final: 0.8149 (t0) outliers start: 94 outliers final: 44 residues processed: 296 average time/residue: 0.2162 time to fit residues: 90.5031 Evaluate side-chains 247 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 ASN D 105 ASN D 262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098052 restraints weight = 14303.108| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.86 r_work: 0.3080 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.225 Angle : 0.667 9.790 12834 Z= 0.319 Chirality : 0.044 0.168 1536 Planarity : 0.006 0.103 1606 Dihedral : 10.612 89.250 1428 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 8.65 % Allowed : 17.91 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.23), residues: 1202 helix: -1.34 (0.19), residues: 646 sheet: -1.79 (0.56), residues: 94 loop : -2.59 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 7 HIS 0.004 0.001 HIS C 62 PHE 0.010 0.001 PHE A 162 TYR 0.015 0.001 TYR C 81 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 213 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 51 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8801 (t) REVERT: A 96 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8620 (tp) REVERT: A 116 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7349 (mp) REVERT: A 120 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8171 (pt) REVERT: A 133 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: A 143 VAL cc_start: 0.9248 (t) cc_final: 0.8844 (p) REVERT: A 216 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 31 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8650 (mt) REVERT: B 56 MET cc_start: 0.8483 (tpp) cc_final: 0.8233 (tpp) REVERT: B 70 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8685 (tt) REVERT: B 96 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 120 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8169 (pt) REVERT: B 123 MET cc_start: 0.8420 (mtt) cc_final: 0.8218 (mtm) REVERT: B 128 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: B 143 VAL cc_start: 0.9281 (t) cc_final: 0.8960 (p) REVERT: C 105 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7975 (m-40) REVERT: C 172 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8068 (p90) REVERT: D 105 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7965 (m-40) REVERT: D 172 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8239 (p90) REVERT: D 249 ASP cc_start: 0.8184 (t0) cc_final: 0.7476 (p0) REVERT: E 22 GLN cc_start: 0.8308 (pp30) cc_final: 0.7762 (mp10) REVERT: E 89 ASN cc_start: 0.8776 (t0) cc_final: 0.8017 (t0) REVERT: F 7 TRP cc_start: 0.8263 (p90) cc_final: 0.7539 (p-90) REVERT: F 22 GLN cc_start: 0.8327 (pp30) cc_final: 0.7929 (mp10) REVERT: F 23 ASP cc_start: 0.8557 (t0) cc_final: 0.7941 (t0) REVERT: F 66 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8464 (mmtt) REVERT: F 68 GLN cc_start: 0.8436 (pp30) cc_final: 0.8088 (pm20) REVERT: F 70 ASN cc_start: 0.6553 (t0) cc_final: 0.6304 (t0) REVERT: F 89 ASN cc_start: 0.8761 (t0) cc_final: 0.8197 (t0) outliers start: 86 outliers final: 44 residues processed: 281 average time/residue: 0.1890 time to fit residues: 75.0180 Evaluate side-chains 254 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 0.0470 chunk 113 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 220 ASN C 262 HIS D 262 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098431 restraints weight = 14175.060| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.90 r_work: 0.3070 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9436 Z= 0.208 Angle : 0.653 11.563 12834 Z= 0.312 Chirality : 0.044 0.137 1536 Planarity : 0.006 0.102 1606 Dihedral : 9.968 89.833 1421 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 8.55 % Allowed : 19.82 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.23), residues: 1202 helix: -1.09 (0.19), residues: 664 sheet: -1.61 (0.55), residues: 94 loop : -2.37 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 7 HIS 0.005 0.001 HIS D 62 PHE 0.012 0.001 PHE B 162 TYR 0.016 0.001 TYR D 81 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 217 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 96 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8640 (tp) REVERT: A 98 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7484 (tt0) REVERT: A 116 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 120 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8115 (pt) REVERT: A 216 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 31 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8629 (mt) REVERT: B 84 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7041 (pp20) REVERT: B 96 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 120 ILE cc_start: 0.8732 (pt) cc_final: 0.8189 (pt) REVERT: B 123 MET cc_start: 0.8312 (mtt) cc_final: 0.8087 (mtm) REVERT: B 132 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: C 51 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 105 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7919 (m110) REVERT: C 143 SER cc_start: 0.8594 (t) cc_final: 0.8381 (p) REVERT: C 172 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8068 (p90) REVERT: D 105 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7893 (m110) REVERT: D 143 SER cc_start: 0.8645 (t) cc_final: 0.8406 (p) REVERT: D 172 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8130 (p90) REVERT: D 249 ASP cc_start: 0.8180 (t0) cc_final: 0.7450 (p0) REVERT: E 23 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8353 (t0) REVERT: E 66 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8279 (tppt) REVERT: E 89 ASN cc_start: 0.8829 (t0) cc_final: 0.8048 (t0) REVERT: F 7 TRP cc_start: 0.8219 (p90) cc_final: 0.7682 (p-90) REVERT: F 23 ASP cc_start: 0.8535 (t0) cc_final: 0.8279 (t0) REVERT: F 68 GLN cc_start: 0.8375 (pp30) cc_final: 0.8121 (pm20) REVERT: F 89 ASN cc_start: 0.8783 (t0) cc_final: 0.8194 (t0) outliers start: 85 outliers final: 50 residues processed: 285 average time/residue: 0.2175 time to fit residues: 88.9091 Evaluate side-chains 261 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.0070 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 220 ASN C 262 HIS D 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099399 restraints weight = 14091.928| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.90 r_work: 0.3081 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9436 Z= 0.213 Angle : 0.635 9.654 12834 Z= 0.310 Chirality : 0.043 0.144 1536 Planarity : 0.005 0.100 1606 Dihedral : 9.810 84.650 1416 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.85 % Allowed : 21.03 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.23), residues: 1202 helix: -0.86 (0.19), residues: 662 sheet: -1.55 (0.54), residues: 94 loop : -2.35 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 215 HIS 0.007 0.001 HIS D 113 PHE 0.010 0.001 PHE A 162 TYR 0.006 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 216 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8629 (mt) REVERT: A 98 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7570 (tt0) REVERT: A 116 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7508 (mp) REVERT: A 120 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8197 (pt) REVERT: A 133 GLU cc_start: 0.8532 (tt0) cc_final: 0.8314 (tt0) REVERT: A 197 MET cc_start: 0.7022 (tpp) cc_final: 0.6744 (tpp) REVERT: A 201 ASN cc_start: 0.7983 (m110) cc_final: 0.7731 (m-40) REVERT: A 216 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 257 MET cc_start: 0.8077 (mtm) cc_final: 0.7610 (mtm) REVERT: B 31 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 56 MET cc_start: 0.8474 (tpp) cc_final: 0.8268 (tpp) REVERT: B 96 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 120 ILE cc_start: 0.8724 (pt) cc_final: 0.8158 (pt) REVERT: B 123 MET cc_start: 0.8338 (mtt) cc_final: 0.8129 (mtm) REVERT: C 105 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7898 (m110) REVERT: C 143 SER cc_start: 0.8553 (t) cc_final: 0.8334 (p) REVERT: C 172 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7887 (p90) REVERT: D 105 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7970 (m110) REVERT: D 143 SER cc_start: 0.8615 (t) cc_final: 0.8394 (p) REVERT: D 172 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8101 (p90) REVERT: D 249 ASP cc_start: 0.8163 (t0) cc_final: 0.7489 (p0) REVERT: E 22 GLN cc_start: 0.8261 (pp30) cc_final: 0.7864 (mp10) REVERT: E 23 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: E 66 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8298 (tppt) REVERT: E 89 ASN cc_start: 0.8854 (t0) cc_final: 0.8045 (t0) REVERT: F 7 TRP cc_start: 0.8235 (p90) cc_final: 0.7640 (p-90) REVERT: F 22 GLN cc_start: 0.8261 (pp30) cc_final: 0.7874 (mp10) REVERT: F 23 ASP cc_start: 0.8516 (t0) cc_final: 0.7976 (t0) REVERT: F 66 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8295 (tppt) REVERT: F 89 ASN cc_start: 0.8840 (t0) cc_final: 0.8248 (t0) outliers start: 78 outliers final: 47 residues processed: 278 average time/residue: 0.2072 time to fit residues: 79.8999 Evaluate side-chains 258 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100023 restraints weight = 14083.240| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.84 r_work: 0.3111 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9436 Z= 0.226 Angle : 0.641 9.720 12834 Z= 0.310 Chirality : 0.043 0.165 1536 Planarity : 0.005 0.098 1606 Dihedral : 9.529 89.506 1413 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.95 % Allowed : 21.03 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.24), residues: 1202 helix: -0.68 (0.20), residues: 664 sheet: -1.54 (0.53), residues: 94 loop : -2.22 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 195 HIS 0.005 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.008 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 98 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7667 (tt0) REVERT: A 116 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 120 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8423 (pt) REVERT: A 133 GLU cc_start: 0.8492 (tt0) cc_final: 0.8278 (tt0) REVERT: A 216 ILE cc_start: 0.8736 (pp) cc_final: 0.8354 (mm) REVERT: A 257 MET cc_start: 0.7742 (mtm) cc_final: 0.7501 (mtm) REVERT: B 31 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 56 MET cc_start: 0.8491 (tpp) cc_final: 0.8275 (tpp) REVERT: B 96 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8275 (tt) REVERT: B 120 ILE cc_start: 0.8726 (pt) cc_final: 0.8181 (pt) REVERT: B 123 MET cc_start: 0.8429 (mtt) cc_final: 0.8182 (mtm) REVERT: B 191 ASN cc_start: 0.7343 (m-40) cc_final: 0.6987 (p0) REVERT: B 198 ASP cc_start: 0.8066 (t0) cc_final: 0.7763 (t0) REVERT: C 51 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 105 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (m110) REVERT: C 143 SER cc_start: 0.8587 (t) cc_final: 0.8366 (p) REVERT: C 172 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7903 (p90) REVERT: C 207 GLU cc_start: 0.8236 (mp0) cc_final: 0.7946 (mp0) REVERT: D 143 SER cc_start: 0.8550 (t) cc_final: 0.8340 (p) REVERT: D 249 ASP cc_start: 0.8161 (t0) cc_final: 0.7566 (p0) REVERT: E 22 GLN cc_start: 0.8271 (pp30) cc_final: 0.7795 (mp10) REVERT: E 66 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8267 (tppt) REVERT: E 89 ASN cc_start: 0.8867 (t0) cc_final: 0.8007 (t0) REVERT: F 7 TRP cc_start: 0.8258 (p90) cc_final: 0.7556 (p-90) REVERT: F 22 GLN cc_start: 0.8261 (pp30) cc_final: 0.7848 (mp10) REVERT: F 23 ASP cc_start: 0.8546 (t0) cc_final: 0.7983 (t0) REVERT: F 66 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8237 (tppt) REVERT: F 89 ASN cc_start: 0.8863 (t0) cc_final: 0.8255 (t0) outliers start: 79 outliers final: 57 residues processed: 277 average time/residue: 0.2336 time to fit residues: 89.7179 Evaluate side-chains 261 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100135 restraints weight = 14143.616| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.91 r_work: 0.3091 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9436 Z= 0.207 Angle : 0.636 10.845 12834 Z= 0.308 Chirality : 0.043 0.171 1536 Planarity : 0.005 0.095 1606 Dihedral : 9.191 84.486 1411 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.34 % Allowed : 22.03 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.24), residues: 1202 helix: -0.43 (0.20), residues: 652 sheet: -1.48 (0.53), residues: 94 loop : -1.97 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 7 HIS 0.003 0.001 HIS D 62 PHE 0.011 0.001 PHE A 162 TYR 0.005 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8586 (mt) REVERT: A 98 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7564 (tt0) REVERT: A 116 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 197 MET cc_start: 0.7068 (tpp) cc_final: 0.6547 (tpp) REVERT: A 216 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8403 (mm) REVERT: B 31 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 56 MET cc_start: 0.8415 (tpp) cc_final: 0.8192 (tpp) REVERT: B 73 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: B 96 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 98 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7524 (tt0) REVERT: B 123 MET cc_start: 0.8342 (mtt) cc_final: 0.8088 (mtm) REVERT: B 191 ASN cc_start: 0.7374 (m-40) cc_final: 0.6987 (p0) REVERT: B 198 ASP cc_start: 0.8138 (t0) cc_final: 0.7735 (t0) REVERT: B 257 MET cc_start: 0.8353 (mtm) cc_final: 0.7821 (mtp) REVERT: C 51 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 105 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8104 (m110) REVERT: C 207 GLU cc_start: 0.8226 (mp0) cc_final: 0.7962 (mp0) REVERT: C 235 ASN cc_start: 0.8283 (t0) cc_final: 0.8075 (t0) REVERT: D 172 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7972 (p90) REVERT: D 249 ASP cc_start: 0.8079 (t0) cc_final: 0.7503 (p0) REVERT: E 66 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8255 (tppt) REVERT: E 89 ASN cc_start: 0.8870 (t0) cc_final: 0.8279 (t0) REVERT: F 7 TRP cc_start: 0.8266 (p90) cc_final: 0.7553 (p-90) REVERT: F 22 GLN cc_start: 0.8189 (pp30) cc_final: 0.7966 (mp10) REVERT: F 23 ASP cc_start: 0.8533 (t0) cc_final: 0.8084 (t0) REVERT: F 66 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8206 (tppt) REVERT: F 89 ASN cc_start: 0.8876 (t0) cc_final: 0.8273 (t0) outliers start: 73 outliers final: 55 residues processed: 271 average time/residue: 0.2135 time to fit residues: 79.4369 Evaluate side-chains 259 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100370 restraints weight = 14220.293| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.92 r_work: 0.3092 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9436 Z= 0.205 Angle : 0.638 9.651 12834 Z= 0.308 Chirality : 0.043 0.165 1536 Planarity : 0.005 0.094 1606 Dihedral : 8.750 74.513 1408 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.44 % Allowed : 22.13 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.24), residues: 1202 helix: -0.27 (0.20), residues: 650 sheet: -1.22 (0.58), residues: 84 loop : -1.97 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 7 HIS 0.003 0.001 HIS D 62 PHE 0.011 0.001 PHE B 162 TYR 0.007 0.001 TYR C 261 ARG 0.007 0.000 ARG D 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 1.011 Fit side-chains REVERT: A 31 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8528 (mt) REVERT: A 98 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7588 (tt0) REVERT: A 116 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 201 ASN cc_start: 0.8019 (m-40) cc_final: 0.7690 (m-40) REVERT: A 216 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 56 MET cc_start: 0.8417 (tpp) cc_final: 0.8198 (tpp) REVERT: B 73 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: B 98 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7537 (tt0) REVERT: B 123 MET cc_start: 0.8343 (mtt) cc_final: 0.8086 (mtm) REVERT: B 191 ASN cc_start: 0.7367 (m-40) cc_final: 0.6997 (p0) REVERT: C 51 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 207 GLU cc_start: 0.8128 (mp0) cc_final: 0.7850 (mp0) REVERT: D 249 ASP cc_start: 0.8130 (t0) cc_final: 0.7541 (p0) REVERT: E 66 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8259 (tppt) REVERT: E 89 ASN cc_start: 0.8855 (t0) cc_final: 0.8210 (t0) REVERT: F 7 TRP cc_start: 0.8264 (p90) cc_final: 0.7555 (p-90) REVERT: F 23 ASP cc_start: 0.8485 (t0) cc_final: 0.7989 (t0) REVERT: F 66 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8134 (tppt) REVERT: F 89 ASN cc_start: 0.8865 (t0) cc_final: 0.8254 (t0) outliers start: 74 outliers final: 60 residues processed: 265 average time/residue: 0.2105 time to fit residues: 77.8798 Evaluate side-chains 263 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 97 optimal weight: 0.0060 chunk 17 optimal weight: 7.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104887 restraints weight = 13488.722| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.93 r_work: 0.3152 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9436 Z= 0.201 Angle : 0.637 9.657 12834 Z= 0.308 Chirality : 0.043 0.157 1536 Planarity : 0.005 0.092 1606 Dihedral : 8.156 61.574 1404 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 6.54 % Allowed : 23.64 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.24), residues: 1202 helix: -0.17 (0.20), residues: 662 sheet: -1.10 (0.60), residues: 84 loop : -2.01 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 7 HIS 0.002 0.001 HIS D 62 PHE 0.010 0.001 PHE A 162 TYR 0.005 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 0.952 Fit side-chains REVERT: A 31 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 98 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7602 (tt0) REVERT: A 116 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 201 ASN cc_start: 0.7942 (m-40) cc_final: 0.7671 (m-40) REVERT: A 216 ILE cc_start: 0.8643 (pp) cc_final: 0.8304 (mm) REVERT: A 257 MET cc_start: 0.8402 (ttp) cc_final: 0.8003 (ttm) REVERT: B 56 MET cc_start: 0.8417 (tpp) cc_final: 0.8167 (tpp) REVERT: B 73 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: B 98 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7535 (tt0) REVERT: B 123 MET cc_start: 0.8313 (mtt) cc_final: 0.8063 (mtm) REVERT: B 191 ASN cc_start: 0.7384 (m-40) cc_final: 0.6987 (p0) REVERT: B 197 MET cc_start: 0.6969 (tpp) cc_final: 0.6526 (tpp) REVERT: C 51 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 75 MET cc_start: 0.7921 (mtt) cc_final: 0.7580 (mtt) REVERT: C 83 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8993 (p) REVERT: C 207 GLU cc_start: 0.8160 (mp0) cc_final: 0.7910 (mp0) REVERT: D 12 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7854 (mmt90) REVERT: D 83 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8958 (p) REVERT: D 89 MET cc_start: 0.8478 (mtp) cc_final: 0.8272 (mtp) REVERT: D 172 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.7853 (p90) REVERT: D 207 GLU cc_start: 0.8061 (mp0) cc_final: 0.7814 (mp0) REVERT: D 249 ASP cc_start: 0.8177 (t0) cc_final: 0.7548 (p0) REVERT: D 252 VAL cc_start: 0.8834 (t) cc_final: 0.8547 (p) REVERT: E 31 MET cc_start: 0.8168 (pmm) cc_final: 0.7819 (pmm) REVERT: E 66 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8176 (tppt) REVERT: E 89 ASN cc_start: 0.8780 (t0) cc_final: 0.8096 (t0) REVERT: F 7 TRP cc_start: 0.8236 (p90) cc_final: 0.7530 (p-90) REVERT: F 66 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8071 (tppt) REVERT: F 89 ASN cc_start: 0.8823 (t0) cc_final: 0.8189 (t0) outliers start: 65 outliers final: 55 residues processed: 262 average time/residue: 0.2085 time to fit residues: 74.9426 Evaluate side-chains 265 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 100 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102050 restraints weight = 13750.836| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.94 r_work: 0.3105 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9436 Z= 0.265 Angle : 0.666 9.749 12834 Z= 0.322 Chirality : 0.044 0.166 1536 Planarity : 0.005 0.095 1606 Dihedral : 8.179 59.668 1400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 6.54 % Allowed : 23.44 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.24), residues: 1202 helix: -0.21 (0.20), residues: 662 sheet: -1.32 (0.55), residues: 94 loop : -1.99 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 7 HIS 0.003 0.001 HIS D 113 PHE 0.013 0.001 PHE B 162 TYR 0.008 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7621 (tt0) REVERT: A 116 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7467 (mp) REVERT: A 120 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8528 (pt) REVERT: A 216 ILE cc_start: 0.8671 (pp) cc_final: 0.8319 (mm) REVERT: B 56 MET cc_start: 0.8430 (tpp) cc_final: 0.8175 (tpp) REVERT: B 73 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: B 98 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7632 (tt0) REVERT: B 120 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8234 (pt) REVERT: B 123 MET cc_start: 0.8396 (mtt) cc_final: 0.8144 (mtm) REVERT: B 191 ASN cc_start: 0.7398 (m-40) cc_final: 0.6997 (p0) REVERT: B 201 ASN cc_start: 0.8069 (m-40) cc_final: 0.7829 (m-40) REVERT: C 51 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 75 MET cc_start: 0.7927 (mtt) cc_final: 0.7582 (mtt) REVERT: C 83 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9015 (p) REVERT: C 207 GLU cc_start: 0.8229 (mp0) cc_final: 0.7980 (mp0) REVERT: D 12 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7914 (mmt90) REVERT: D 83 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8974 (p) REVERT: D 89 MET cc_start: 0.8521 (mtp) cc_final: 0.8262 (mtp) REVERT: D 249 ASP cc_start: 0.8188 (t0) cc_final: 0.7572 (p0) REVERT: E 31 MET cc_start: 0.8254 (pmm) cc_final: 0.7969 (pmm) REVERT: E 66 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8151 (tppt) REVERT: F 22 GLN cc_start: 0.8189 (pp30) cc_final: 0.7952 (mp10) REVERT: F 66 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8092 (tppt) REVERT: F 89 ASN cc_start: 0.8768 (t0) cc_final: 0.8401 (t0) outliers start: 65 outliers final: 54 residues processed: 248 average time/residue: 0.2138 time to fit residues: 72.7067 Evaluate side-chains 256 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101009 restraints weight = 14034.382| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.90 r_work: 0.3103 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9436 Z= 0.214 Angle : 0.660 9.699 12834 Z= 0.317 Chirality : 0.043 0.158 1536 Planarity : 0.005 0.090 1606 Dihedral : 7.926 58.520 1398 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 6.24 % Allowed : 24.25 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.25), residues: 1202 helix: -0.05 (0.20), residues: 658 sheet: -0.96 (0.61), residues: 84 loop : -1.96 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 7 HIS 0.002 0.001 HIS D 62 PHE 0.011 0.001 PHE B 162 TYR 0.006 0.001 TYR C 261 ARG 0.007 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4830.70 seconds wall clock time: 85 minutes 33.45 seconds (5133.45 seconds total)