Starting phenix.real_space_refine on Sun Jul 27 10:47:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch6_30369/07_2025/7ch6_30369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch6_30369/07_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_30369/07_2025/7ch6_30369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch6_30369/07_2025/7ch6_30369.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch6_30369/07_2025/7ch6_30369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch6_30369/07_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-5711/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: 6.26, per 1000 atoms: 0.68 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: 2.57 Conformation dependent library (CDL) restraints added in 1.3 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: 0.99 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: 2.52 Time building geometry restraints manager: 2.85 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: 1.990 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.920 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- 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= 0.355 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 Details of bonding type rmsd hydrogen bonds : bond 0.17489 ( 422) hydrogen bonds : angle 8.62026 ( 1254) covalent geometry : bond 0.00784 ( 9436) covalent geometry : angle 0.82134 (12834) *********************** 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 : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8652 (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: 0.8462 (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: 0.7361 (mp) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7885 (mtm) REVERT: A 244 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8429 (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: 0.8687 (mt) REVERT: B 70 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8685 (tt) REVERT: B 96 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 116 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7383 (mp) REVERT: B 123 MET cc_start: 0.8040 (mtt) cc_final: 0.7767 (mtm) REVERT: B 244 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8466 (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: 0.8502 (p0) REVERT: C 178 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8876 (tt) REVERT: D 170 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: D 249 ASP cc_start: 0.7664 (t0) cc_final: 0.7359 (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: 0.7831 (t0) outliers start: 128 outliers final: 47 residues processed: 356 average time/residue: 0.2117 time to fit residues: 103.2181 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 : 0.936 ------------------------------------------------------------------------------- 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: 0.0970 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: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.119198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097737 restraints weight = 14080.201| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.84 r_work: 0.3072 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2245 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= 0.148 Angle : 0.725 9.824 12834 Z= 0.344 Chirality : 0.045 0.153 1536 Planarity : 0.006 0.107 1606 Dihedral : 13.053 91.038 1471 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 10.06 % Allowed : 16.30 % Favored : 73.64 % 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: -3.31 (0.22), residues: 1202 helix: -1.71 (0.18), residues: 652 sheet: -2.15 (0.61), residues: 78 loop : -2.76 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 7 HIS 0.006 0.001 HIS C 113 PHE 0.013 0.001 PHE C 91 TYR 0.013 0.001 TYR D 81 ARG 0.009 0.001 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 422) hydrogen bonds : angle 5.93806 ( 1254) covalent geometry : bond 0.00338 ( 9436) covalent geometry : angle 0.72510 (12834) *********************** 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 324 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 224 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 51 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8777 (t) REVERT: A 96 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8433 (tt) REVERT: A 116 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7474 (mp) REVERT: A 120 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8219 (pt) REVERT: A 123 MET cc_start: 0.8443 (mtt) cc_final: 0.8227 (mtm) REVERT: A 134 MET cc_start: 0.9053 (tpt) cc_final: 0.8690 (tpt) REVERT: A 198 ASP cc_start: 0.8080 (t0) cc_final: 0.7787 (t0) REVERT: A 216 ILE cc_start: 0.8762 (pp) cc_final: 0.8218 (mm) REVERT: B 31 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8723 (mt) REVERT: B 70 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8708 (tt) REVERT: B 96 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 120 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8186 (pt) REVERT: B 123 MET cc_start: 0.8401 (mtt) cc_final: 0.8165 (mtm) REVERT: B 134 MET cc_start: 0.8889 (tpt) cc_final: 0.8520 (tpt) REVERT: B 198 ASP cc_start: 0.8069 (t0) cc_final: 0.7683 (t0) REVERT: B 216 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8526 (tp) REVERT: C 105 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: C 172 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7931 (p90) REVERT: C 207 GLU cc_start: 0.8083 (mp0) cc_final: 0.7754 (mp0) REVERT: D 105 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7945 (m-40) REVERT: D 172 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8116 (p90) REVERT: D 249 ASP cc_start: 0.8219 (t0) cc_final: 0.7542 (p0) REVERT: E 89 ASN cc_start: 0.8760 (t0) cc_final: 0.8013 (t0) REVERT: F 22 GLN cc_start: 0.8449 (pp30) cc_final: 0.7920 (mp10) REVERT: F 66 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8331 (mmtm) REVERT: F 89 ASN cc_start: 0.8730 (t0) cc_final: 0.8163 (t0) outliers start: 100 outliers final: 45 residues processed: 307 average time/residue: 0.1926 time to fit residues: 82.9698 Evaluate side-chains 254 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 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 216 ILE 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 57 LEU Chi-restraints excluded: chain E residue 64 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 57 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: 1.9990 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 ASN C 214 HIS C 262 HIS D 105 ASN D 175 GLN D 214 HIS D 262 HIS E 71 ASN F 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098809 restraints weight = 14303.837| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.86 r_work: 0.3093 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2798 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= 0.139 Angle : 0.666 9.729 12834 Z= 0.318 Chirality : 0.045 0.143 1536 Planarity : 0.006 0.101 1606 Dihedral : 11.082 86.778 1430 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 8.15 % Allowed : 19.52 % Favored : 72.33 % 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: -2.75 (0.23), residues: 1202 helix: -1.29 (0.19), residues: 660 sheet: -1.76 (0.56), residues: 94 loop : -2.50 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 7 HIS 0.005 0.001 HIS C 62 PHE 0.011 0.001 PHE A 162 TYR 0.011 0.001 TYR D 81 ARG 0.007 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 422) hydrogen bonds : angle 5.54271 ( 1254) covalent geometry : bond 0.00329 ( 9436) covalent geometry : angle 0.66598 (12834) *********************** 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 294 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 213 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8646 (mt) REVERT: A 51 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8811 (t) REVERT: A 96 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 116 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 120 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8086 (pt) REVERT: A 133 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: A 216 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 31 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8665 (mt) REVERT: B 70 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 96 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8450 (tt) REVERT: B 120 ILE cc_start: 0.8761 (pt) cc_final: 0.8208 (pt) REVERT: B 123 MET cc_start: 0.8405 (mtt) cc_final: 0.8164 (mtm) REVERT: B 216 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8568 (tp) REVERT: C 105 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7951 (m-40) REVERT: C 172 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8103 (p90) REVERT: D 105 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7898 (m-40) REVERT: D 172 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8197 (p90) REVERT: D 249 ASP cc_start: 0.8189 (t0) cc_final: 0.7463 (p0) REVERT: E 7 TRP cc_start: 0.8181 (p90) cc_final: 0.7722 (p-90) REVERT: E 22 GLN cc_start: 0.8307 (pp30) cc_final: 0.7785 (mp10) REVERT: E 89 ASN cc_start: 0.8770 (t0) cc_final: 0.7999 (t0) REVERT: F 7 TRP cc_start: 0.8222 (p90) cc_final: 0.7539 (p-90) REVERT: F 22 GLN cc_start: 0.8337 (pp30) cc_final: 0.7828 (mp10) REVERT: F 66 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8186 (tppt) REVERT: F 68 GLN cc_start: 0.8382 (pp30) cc_final: 0.8032 (pm20) REVERT: F 89 ASN cc_start: 0.8778 (t0) cc_final: 0.8229 (t0) outliers start: 81 outliers final: 41 residues processed: 276 average time/residue: 0.2359 time to fit residues: 90.6046 Evaluate side-chains 244 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 44 LEU 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 216 ILE 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 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 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 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: 7.9990 chunk 113 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 262 HIS D 214 HIS D 262 HIS F 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097473 restraints weight = 14239.288| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.90 r_work: 0.3056 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9436 Z= 0.153 Angle : 0.661 11.427 12834 Z= 0.316 Chirality : 0.044 0.139 1536 Planarity : 0.006 0.104 1606 Dihedral : 10.248 86.491 1418 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 9.36 % Allowed : 18.51 % Favored : 72.13 % 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: -2.50 (0.23), residues: 1202 helix: -1.07 (0.19), residues: 662 sheet: -1.64 (0.55), residues: 94 loop : -2.41 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 7 HIS 0.005 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.010 0.001 TYR C 81 ARG 0.007 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 422) hydrogen bonds : angle 5.45895 ( 1254) covalent geometry : bond 0.00372 ( 9436) covalent geometry : angle 0.66060 (12834) *********************** 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 301 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 208 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8654 (mt) REVERT: A 96 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8392 (tt) REVERT: A 116 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7384 (mp) REVERT: A 120 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8140 (pt) REVERT: A 128 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: A 133 GLU cc_start: 0.8519 (tt0) cc_final: 0.8285 (tt0) REVERT: A 216 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (mm) REVERT: B 31 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 84 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7064 (pp20) REVERT: B 96 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8444 (tt) REVERT: B 120 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8261 (pt) REVERT: B 123 MET cc_start: 0.8310 (mtt) cc_final: 0.8101 (mtm) REVERT: B 128 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: B 216 ILE cc_start: 0.8847 (pp) cc_final: 0.8350 (mm) REVERT: C 51 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8353 (mp) REVERT: C 105 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7897 (m110) REVERT: C 172 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8015 (p90) REVERT: D 105 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7935 (m110) REVERT: D 172 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8111 (p90) REVERT: D 249 ASP cc_start: 0.8183 (t0) cc_final: 0.7456 (p0) REVERT: E 7 TRP cc_start: 0.8266 (p90) cc_final: 0.7691 (p-90) REVERT: E 68 GLN cc_start: 0.8395 (pm20) cc_final: 0.7967 (pm20) REVERT: E 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8004 (t0) REVERT: F 7 TRP cc_start: 0.8248 (p90) cc_final: 0.7525 (p-90) REVERT: F 23 ASP cc_start: 0.8573 (t0) cc_final: 0.8313 (t0) REVERT: F 68 GLN cc_start: 0.8343 (pp30) cc_final: 0.8094 (pm20) REVERT: F 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8189 (t0) outliers start: 93 outliers final: 52 residues processed: 284 average time/residue: 0.2146 time to fit residues: 86.0273 Evaluate side-chains 264 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 128 GLN Chi-restraints excluded: chain A residue 137 VAL 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 44 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 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET 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 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 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 218 LEU 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 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: 10.0000 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 220 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 262 HIS F 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098249 restraints weight = 14164.745| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.90 r_work: 0.3064 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3160 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= 0.147 Angle : 0.649 9.778 12834 Z= 0.313 Chirality : 0.044 0.142 1536 Planarity : 0.006 0.101 1606 Dihedral : 9.902 87.426 1417 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 8.35 % Allowed : 20.32 % Favored : 71.33 % 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: -2.30 (0.23), residues: 1202 helix: -0.89 (0.19), residues: 664 sheet: -1.70 (0.52), residues: 94 loop : -2.33 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 195 HIS 0.006 0.001 HIS D 113 PHE 0.013 0.001 PHE B 162 TYR 0.007 0.001 TYR C 261 ARG 0.006 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 422) hydrogen bonds : angle 5.35125 ( 1254) covalent geometry : bond 0.00356 ( 9436) covalent geometry : angle 0.64910 (12834) *********************** 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 290 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8636 (mt) REVERT: A 98 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7494 (tt0) REVERT: A 116 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 120 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8132 (pt) REVERT: A 128 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: A 133 GLU cc_start: 0.8515 (tt0) cc_final: 0.8302 (tt0) REVERT: A 134 MET cc_start: 0.9050 (tpt) cc_final: 0.8811 (tpt) REVERT: A 197 MET cc_start: 0.7044 (tpp) cc_final: 0.6800 (tpp) REVERT: A 201 ASN cc_start: 0.7867 (m110) cc_final: 0.7572 (m-40) REVERT: A 216 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 257 MET cc_start: 0.7991 (mtm) cc_final: 0.7723 (mtm) REVERT: B 31 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8572 (mt) REVERT: B 96 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8439 (tt) REVERT: B 120 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8161 (pt) REVERT: B 123 MET cc_start: 0.8329 (mtt) cc_final: 0.8124 (mtm) REVERT: B 128 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 216 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8334 (mm) REVERT: C 51 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 105 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7958 (m110) REVERT: C 143 SER cc_start: 0.8582 (t) cc_final: 0.8378 (p) REVERT: C 172 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7883 (p90) REVERT: D 105 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8034 (m110) REVERT: D 143 SER cc_start: 0.8640 (t) cc_final: 0.8408 (p) REVERT: D 249 ASP cc_start: 0.8180 (t0) cc_final: 0.7487 (p0) REVERT: E 7 TRP cc_start: 0.8245 (p90) cc_final: 0.7638 (p-90) REVERT: E 22 GLN cc_start: 0.8254 (pp30) cc_final: 0.7844 (mp10) REVERT: E 89 ASN cc_start: 0.8831 (t0) cc_final: 0.8001 (t0) REVERT: F 7 TRP cc_start: 0.8338 (p90) cc_final: 0.7666 (p-90) REVERT: F 22 GLN cc_start: 0.8296 (pp30) cc_final: 0.7849 (mp10) REVERT: F 23 ASP cc_start: 0.8546 (t0) cc_final: 0.7962 (t0) REVERT: F 89 ASN cc_start: 0.8834 (t0) cc_final: 0.8211 (t0) outliers start: 83 outliers final: 52 residues processed: 273 average time/residue: 0.2448 time to fit residues: 96.5059 Evaluate side-chains 263 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 128 GLN 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 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 ILE 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 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 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 218 LEU 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 71 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 0.1980 chunk 117 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099936 restraints weight = 13997.867| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.90 r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9436 Z= 0.131 Angle : 0.638 9.683 12834 Z= 0.308 Chirality : 0.043 0.159 1536 Planarity : 0.005 0.096 1606 Dihedral : 9.339 77.629 1415 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 8.15 % Allowed : 20.62 % Favored : 71.23 % 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: -2.03 (0.24), residues: 1202 helix: -0.64 (0.20), residues: 662 sheet: -1.40 (0.57), residues: 84 loop : -2.30 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 195 HIS 0.006 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.006 0.001 TYR D 261 ARG 0.007 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 422) hydrogen bonds : angle 5.22933 ( 1254) covalent geometry : bond 0.00316 ( 9436) covalent geometry : angle 0.63804 (12834) *********************** 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 295 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 214 time to evaluate : 1.074 Fit side-chains REVERT: A 31 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8582 (mt) REVERT: A 98 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7554 (tt0) REVERT: A 116 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7485 (mp) REVERT: A 216 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8261 (mm) REVERT: B 31 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8602 (mt) REVERT: B 73 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: B 120 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8246 (pt) REVERT: B 128 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: B 191 ASN cc_start: 0.7376 (m-40) cc_final: 0.6994 (p0) REVERT: B 216 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8361 (mm) REVERT: C 51 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 105 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8087 (m110) REVERT: C 143 SER cc_start: 0.8589 (t) cc_final: 0.8387 (p) REVERT: C 207 GLU cc_start: 0.8227 (mp0) cc_final: 0.7925 (mp0) REVERT: C 262 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6945 (m-70) REVERT: D 105 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8064 (m110) REVERT: D 143 SER cc_start: 0.8561 (t) cc_final: 0.8357 (p) REVERT: D 172 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8079 (p90) REVERT: D 249 ASP cc_start: 0.8186 (t0) cc_final: 0.7560 (p0) REVERT: E 7 TRP cc_start: 0.8246 (p90) cc_final: 0.7692 (p-90) REVERT: E 22 GLN cc_start: 0.8183 (pp30) cc_final: 0.7863 (mp10) REVERT: E 89 ASN cc_start: 0.8868 (t0) cc_final: 0.7982 (t0) REVERT: F 7 TRP cc_start: 0.8309 (p90) cc_final: 0.7649 (p-90) REVERT: F 22 GLN cc_start: 0.8226 (pp30) cc_final: 0.7902 (mp10) REVERT: F 23 ASP cc_start: 0.8547 (t0) cc_final: 0.8017 (t0) REVERT: F 89 ASN cc_start: 0.8890 (t0) cc_final: 0.8294 (t0) outliers start: 81 outliers final: 53 residues processed: 277 average time/residue: 0.2037 time to fit residues: 78.9788 Evaluate side-chains 264 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 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 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 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 C residue 262 HIS 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 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 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 218 LEU 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 47 VAL Chi-restraints excluded: chain E residue 52 THR 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 52 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: 1.9990 chunk 46 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.0060 chunk 43 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** 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 = 0.3521 r_free = 0.3521 target = 0.122182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100443 restraints weight = 14062.800| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.89 r_work: 0.3097 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3522 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= 0.131 Angle : 0.637 9.700 12834 Z= 0.307 Chirality : 0.043 0.168 1536 Planarity : 0.005 0.094 1606 Dihedral : 8.864 68.496 1408 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 7.65 % Allowed : 22.33 % 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: -1.76 (0.24), residues: 1202 helix: -0.45 (0.20), residues: 654 sheet: -1.39 (0.57), residues: 84 loop : -2.08 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 195 HIS 0.005 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.004 0.001 TYR D 261 ARG 0.007 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 422) hydrogen bonds : angle 5.19309 ( 1254) covalent geometry : bond 0.00311 ( 9436) covalent geometry : angle 0.63659 (12834) *********************** 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 282 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 206 time to evaluate : 1.068 Fit side-chains REVERT: A 31 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 98 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7620 (tt0) REVERT: A 116 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7523 (mp) REVERT: A 197 MET cc_start: 0.7045 (tpp) cc_final: 0.6643 (tpp) REVERT: A 216 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 257 MET cc_start: 0.8020 (mtm) cc_final: 0.7739 (mtm) REVERT: B 31 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 73 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: B 98 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7496 (tt0) REVERT: B 128 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: B 191 ASN cc_start: 0.7394 (m-40) cc_final: 0.6999 (p0) REVERT: B 197 MET cc_start: 0.7242 (tpp) cc_final: 0.6811 (tpp) REVERT: B 216 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8314 (mm) REVERT: C 51 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8257 (mp) REVERT: C 207 GLU cc_start: 0.8232 (mp0) cc_final: 0.7963 (mp0) REVERT: C 262 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6985 (m-70) REVERT: D 172 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7980 (p90) REVERT: D 249 ASP cc_start: 0.8091 (t0) cc_final: 0.7516 (p0) REVERT: D 262 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6765 (m-70) REVERT: E 7 TRP cc_start: 0.8244 (p90) cc_final: 0.7701 (p-90) REVERT: E 22 GLN cc_start: 0.8133 (pp30) cc_final: 0.7894 (mp10) REVERT: E 66 LYS cc_start: 0.8493 (tppt) cc_final: 0.7910 (tptm) REVERT: E 89 ASN cc_start: 0.8867 (t0) cc_final: 0.8228 (t0) REVERT: F 7 TRP cc_start: 0.8310 (p90) cc_final: 0.7601 (p-90) REVERT: F 22 GLN cc_start: 0.8207 (pp30) cc_final: 0.7916 (mp10) REVERT: F 23 ASP cc_start: 0.8528 (t0) cc_final: 0.7936 (t0) REVERT: F 89 ASN cc_start: 0.8885 (t0) cc_final: 0.8285 (t0) outliers start: 76 outliers final: 52 residues processed: 265 average time/residue: 0.2358 time to fit residues: 85.8404 Evaluate side-chains 260 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 128 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 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 92 GLN 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 37 THR 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 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 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 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 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 116 optimal weight: 0.0370 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101144 restraints weight = 14202.623| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.91 r_work: 0.3106 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3646 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= 0.125 Angle : 0.625 9.645 12834 Z= 0.301 Chirality : 0.043 0.149 1536 Planarity : 0.005 0.093 1606 Dihedral : 8.264 60.657 1404 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.94 % Allowed : 22.13 % Favored : 70.93 % 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: -1.58 (0.24), residues: 1202 helix: -0.30 (0.20), residues: 654 sheet: -1.26 (0.58), residues: 84 loop : -2.03 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 195 HIS 0.002 0.001 HIS D 62 PHE 0.013 0.001 PHE B 162 TYR 0.005 0.001 TYR B 222 ARG 0.006 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 422) hydrogen bonds : angle 5.11280 ( 1254) covalent geometry : bond 0.00296 ( 9436) covalent geometry : angle 0.62499 (12834) *********************** 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 278 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 1.040 Fit side-chains REVERT: A 31 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 98 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7634 (tt0) REVERT: A 116 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7416 (mp) REVERT: A 120 ILE cc_start: 0.8691 (pt) cc_final: 0.8175 (pt) REVERT: A 197 MET cc_start: 0.7115 (tpp) cc_final: 0.6681 (tpp) REVERT: A 216 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8313 (mm) REVERT: A 257 MET cc_start: 0.8032 (mtm) cc_final: 0.7733 (mtm) REVERT: B 31 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8609 (mt) REVERT: B 73 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: B 98 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7535 (tt0) REVERT: B 120 ILE cc_start: 0.8718 (pt) cc_final: 0.8100 (pt) REVERT: B 128 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: B 191 ASN cc_start: 0.7377 (m-40) cc_final: 0.7009 (p0) REVERT: B 216 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8327 (mm) REVERT: C 51 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8253 (mp) REVERT: C 75 MET cc_start: 0.7958 (mtt) cc_final: 0.7634 (mtt) REVERT: C 83 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8991 (p) REVERT: C 207 GLU cc_start: 0.8197 (mp0) cc_final: 0.7926 (mp0) REVERT: C 262 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6917 (m-70) REVERT: D 70 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: D 83 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8964 (p) REVERT: D 172 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8003 (p90) REVERT: D 207 GLU cc_start: 0.8088 (mp0) cc_final: 0.7855 (mp0) REVERT: D 249 ASP cc_start: 0.8141 (t0) cc_final: 0.7559 (p0) REVERT: D 252 VAL cc_start: 0.8832 (t) cc_final: 0.8578 (p) REVERT: D 262 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6819 (m-70) REVERT: E 7 TRP cc_start: 0.8230 (p90) cc_final: 0.7655 (p-90) REVERT: E 22 GLN cc_start: 0.8152 (pp30) cc_final: 0.7942 (mp10) REVERT: E 66 LYS cc_start: 0.8354 (tppt) cc_final: 0.7744 (tptm) REVERT: E 89 ASN cc_start: 0.8846 (t0) cc_final: 0.8193 (t0) REVERT: F 7 TRP cc_start: 0.8311 (p90) cc_final: 0.7647 (p-90) REVERT: F 89 ASN cc_start: 0.8852 (t0) cc_final: 0.8256 (t0) outliers start: 69 outliers final: 55 residues processed: 261 average time/residue: 0.2081 time to fit residues: 74.9582 Evaluate side-chains 267 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 54 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 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 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 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 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 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 70 GLU 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 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 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 52 THR 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 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 1 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.124696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102926 restraints weight = 13973.309| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.92 r_work: 0.3132 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3846 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= 0.119 Angle : 0.627 9.614 12834 Z= 0.302 Chirality : 0.042 0.147 1536 Planarity : 0.005 0.090 1606 Dihedral : 7.963 58.834 1404 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 7.14 % Allowed : 22.74 % Favored : 70.12 % 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: -1.39 (0.25), residues: 1202 helix: -0.12 (0.20), residues: 666 sheet: -1.04 (0.60), residues: 84 loop : -2.04 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 195 HIS 0.003 0.001 HIS D 62 PHE 0.012 0.001 PHE B 162 TYR 0.004 0.001 TYR B 222 ARG 0.007 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 422) hydrogen bonds : angle 5.01291 ( 1254) covalent geometry : bond 0.00281 ( 9436) covalent geometry : angle 0.62687 (12834) *********************** 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 278 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 0.950 Fit side-chains REVERT: A 31 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 98 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7611 (tt0) REVERT: A 116 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7503 (mp) REVERT: A 191 ASN cc_start: 0.7314 (m-40) cc_final: 0.6932 (p0) REVERT: A 197 MET cc_start: 0.7140 (tpp) cc_final: 0.6669 (tpp) REVERT: A 216 ILE cc_start: 0.8634 (pp) cc_final: 0.8280 (mm) REVERT: A 257 MET cc_start: 0.7940 (mtm) cc_final: 0.7641 (mtm) REVERT: B 73 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 98 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7543 (tt0) REVERT: B 120 ILE cc_start: 0.8623 (pt) cc_final: 0.8045 (pt) REVERT: B 123 MET cc_start: 0.7876 (mtm) cc_final: 0.7625 (ptp) REVERT: B 128 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: B 191 ASN cc_start: 0.7361 (m-40) cc_final: 0.6998 (p0) REVERT: B 197 MET cc_start: 0.6969 (tpp) cc_final: 0.6701 (tpp) REVERT: B 201 ASN cc_start: 0.7969 (m-40) cc_final: 0.7730 (m-40) REVERT: B 216 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8351 (mm) REVERT: C 75 MET cc_start: 0.7880 (mtt) cc_final: 0.7573 (mtt) REVERT: C 83 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8976 (p) REVERT: C 190 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8031 (mp) REVERT: C 207 GLU cc_start: 0.8105 (mp0) cc_final: 0.7880 (mp0) REVERT: D 70 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: D 83 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8963 (p) REVERT: D 172 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7942 (p90) REVERT: D 190 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8039 (mp) REVERT: D 207 GLU cc_start: 0.8085 (mp0) cc_final: 0.7841 (mp0) REVERT: D 249 ASP cc_start: 0.8077 (t0) cc_final: 0.7566 (p0) REVERT: D 262 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6803 (m-70) REVERT: E 7 TRP cc_start: 0.8175 (p90) cc_final: 0.7707 (p-90) REVERT: E 66 LYS cc_start: 0.8343 (tppt) cc_final: 0.7702 (tptm) REVERT: E 89 ASN cc_start: 0.8826 (t0) cc_final: 0.8166 (t0) REVERT: F 7 TRP cc_start: 0.8271 (p90) cc_final: 0.7628 (p-90) REVERT: F 22 GLN cc_start: 0.8107 (pp30) cc_final: 0.7882 (mp10) REVERT: F 89 ASN cc_start: 0.8883 (t0) cc_final: 0.8317 (t0) outliers start: 71 outliers final: 52 residues processed: 261 average time/residue: 0.2168 time to fit residues: 78.0990 Evaluate side-chains 260 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 96 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 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 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 190 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 70 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN 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 190 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 23 ASP 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 F residue 5 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 ASN D 71 ASN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105116 restraints weight = 13649.739| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.95 r_work: 0.3134 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3871 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= 0.131 Angle : 0.642 9.656 12834 Z= 0.307 Chirality : 0.043 0.146 1536 Planarity : 0.005 0.089 1606 Dihedral : 7.855 59.544 1398 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.64 % Allowed : 23.54 % 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: -1.27 (0.25), residues: 1202 helix: -0.04 (0.20), residues: 662 sheet: -0.88 (0.61), residues: 84 loop : -1.97 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 195 HIS 0.003 0.001 HIS D 62 PHE 0.013 0.001 PHE B 162 TYR 0.004 0.001 TYR A 75 ARG 0.007 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 422) hydrogen bonds : angle 4.98764 ( 1254) covalent geometry : bond 0.00316 ( 9436) covalent geometry : angle 0.64220 (12834) ********************** 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 266 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 1.061 Fit side-chains REVERT: A 98 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7530 (tt0) REVERT: A 116 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7379 (mp) REVERT: A 120 ILE cc_start: 0.8704 (pt) cc_final: 0.8131 (pt) REVERT: A 191 ASN cc_start: 0.7369 (m-40) cc_final: 0.6963 (p0) REVERT: A 197 MET cc_start: 0.7150 (tpp) cc_final: 0.6662 (tpp) REVERT: A 216 ILE cc_start: 0.8653 (pp) cc_final: 0.8278 (mm) REVERT: A 257 MET cc_start: 0.8023 (mtm) cc_final: 0.7711 (mtm) REVERT: B 73 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: B 98 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7556 (tt0) REVERT: B 120 ILE cc_start: 0.8675 (pt) cc_final: 0.8036 (pt) REVERT: B 128 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 191 ASN cc_start: 0.7389 (m-40) cc_final: 0.7002 (p0) REVERT: B 201 ASN cc_start: 0.7957 (m-40) cc_final: 0.7682 (m-40) REVERT: B 216 ILE cc_start: 0.8718 (pp) cc_final: 0.8372 (mm) REVERT: C 51 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8291 (mp) REVERT: C 75 MET cc_start: 0.7841 (mtt) cc_final: 0.7546 (mtt) REVERT: C 83 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 190 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 207 GLU cc_start: 0.8141 (mp0) cc_final: 0.7926 (mp0) REVERT: D 51 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8291 (mp) REVERT: D 70 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: D 83 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8951 (p) REVERT: D 89 MET cc_start: 0.8505 (mtp) cc_final: 0.8255 (mtp) REVERT: D 172 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7946 (p90) REVERT: D 190 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8016 (mp) REVERT: D 249 ASP cc_start: 0.8146 (t0) cc_final: 0.7565 (p0) REVERT: D 262 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6880 (m-70) REVERT: E 7 TRP cc_start: 0.8179 (p90) cc_final: 0.7681 (p-90) REVERT: F 7 TRP cc_start: 0.8352 (p90) cc_final: 0.7644 (p-90) REVERT: F 22 GLN cc_start: 0.8136 (pp30) cc_final: 0.7914 (mp10) REVERT: F 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8175 (t0) outliers start: 66 outliers final: 53 residues processed: 252 average time/residue: 0.2175 time to fit residues: 76.0135 Evaluate side-chains 264 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain B residue 54 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 128 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 MET 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 190 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 51 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 70 GLU 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 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 190 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 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 F residue 5 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.0870 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** 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 = 0.3550 r_free = 0.3550 target = 0.124545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102628 restraints weight = 13981.936| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.92 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3952 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= 0.125 Angle : 0.639 9.651 12834 Z= 0.306 Chirality : 0.043 0.147 1536 Planarity : 0.005 0.085 1606 Dihedral : 7.751 59.627 1398 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.04 % Allowed : 23.34 % Favored : 69.62 % 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: -1.16 (0.25), residues: 1202 helix: 0.03 (0.21), residues: 662 sheet: -0.75 (0.62), residues: 84 loop : -1.92 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 195 HIS 0.002 0.001 HIS D 62 PHE 0.013 0.001 PHE B 162 TYR 0.004 0.001 TYR B 222 ARG 0.007 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 422) hydrogen bonds : angle 4.93998 ( 1254) covalent geometry : bond 0.00299 ( 9436) covalent geometry : angle 0.63918 (12834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5235.85 seconds wall clock time: 93 minutes 2.04 seconds (5582.04 seconds total)