Starting phenix.real_space_refine on Thu Feb 13 19:06:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch6_30369/02_2025/7ch6_30369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch6_30369/02_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_30369/02_2025/7ch6_30369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch6_30369/02_2025/7ch6_30369.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch6_30369/02_2025/7ch6_30369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch6_30369/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.86, per 1000 atoms: 0.63 Number of scatterers: 9260 At special positions: 0 Unit cell: (105.04, 109.2, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 6 15.00 O 1678 8.00 N 1584 7.00 C 5934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.1 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: 0.74 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: 2.53 Time building geometry restraints manager: 3.19 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.660 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.165 9436 Z= 0.524 Angle : 0.821 9.587 12834 Z= 0.451 Chirality : 0.130 4.754 1536 Planarity : 0.006 0.118 1606 Dihedral : 16.465 118.895 3456 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 12.88 % Allowed : 11.87 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.20), residues: 1202 helix: -2.92 (0.15), residues: 650 sheet: -0.75 (0.94), residues: 40 loop : -3.21 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 195 HIS 0.004 0.001 HIS D 113 PHE 0.015 0.002 PHE A 162 TYR 0.011 0.002 TYR D 256 ARG 0.005 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 257 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 51 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 70 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 96 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 116 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7888 (mtm) REVERT: A 244 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 247 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 31 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8686 (mt) REVERT: B 70 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 96 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 116 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7382 (mp) REVERT: B 123 MET cc_start: 0.8040 (mtt) cc_final: 0.7769 (mtm) REVERT: B 244 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 247 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (mm) REVERT: C 170 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: C 176 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (p0) REVERT: C 178 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8872 (tt) REVERT: D 170 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: D 249 ASP cc_start: 0.7664 (t0) cc_final: 0.7358 (p0) REVERT: E 63 ASP cc_start: 0.7917 (t70) cc_final: 0.7700 (t70) REVERT: F 21 ASP cc_start: 0.8688 (p0) cc_final: 0.8117 (p0) REVERT: F 89 ASN cc_start: 0.8389 (t0) cc_final: 0.7832 (t0) outliers start: 128 outliers final: 47 residues processed: 356 average time/residue: 0.2204 time to fit residues: 107.1336 Evaluate side-chains 254 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 190 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 50 ASN A 190 GLN B 47 GLN B 50 ASN B 190 GLN C 214 HIS D 175 GLN D 214 HIS E 75 GLN F 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096840 restraints weight = 14136.097| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.84 r_work: 0.3060 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9436 Z= 0.240 Angle : 0.724 9.710 12834 Z= 0.345 Chirality : 0.045 0.156 1536 Planarity : 0.006 0.109 1606 Dihedral : 12.910 93.084 1471 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 9.46 % Allowed : 17.51 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.22), residues: 1202 helix: -1.75 (0.18), residues: 640 sheet: -2.16 (0.61), residues: 78 loop : -2.85 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 7 HIS 0.007 0.001 HIS C 113 PHE 0.013 0.001 PHE C 91 TYR 0.011 0.001 TYR D 81 ARG 0.014 0.001 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 216 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8692 (mt) REVERT: A 51 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8753 (t) REVERT: A 56 MET cc_start: 0.8455 (ttm) cc_final: 0.8067 (mtt) REVERT: A 96 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 116 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 120 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8341 (pt) REVERT: A 123 MET cc_start: 0.8469 (mtt) cc_final: 0.8243 (mtm) REVERT: B 31 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8721 (mt) REVERT: B 70 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8710 (tt) REVERT: B 96 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8396 (tt) REVERT: B 120 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8240 (pt) REVERT: B 123 MET cc_start: 0.8440 (mtt) cc_final: 0.8204 (mtm) REVERT: B 198 ASP cc_start: 0.8102 (t0) cc_final: 0.7729 (t0) REVERT: C 105 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8016 (m-40) REVERT: C 172 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8015 (p90) REVERT: D 105 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7960 (m-40) REVERT: D 172 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8091 (p90) REVERT: D 249 ASP cc_start: 0.8234 (t0) cc_final: 0.7535 (p0) REVERT: E 89 ASN cc_start: 0.8759 (t0) cc_final: 0.7997 (t0) REVERT: F 89 ASN cc_start: 0.8726 (t0) cc_final: 0.8145 (t0) outliers start: 94 outliers final: 44 residues processed: 296 average time/residue: 0.1977 time to fit residues: 82.1522 Evaluate side-chains 247 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 117 optimal weight: 0.0670 chunk 86 optimal weight: 0.6980 overall best weight: 0.3518 ------------------------------------------------------------------------------- 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 D 105 ASN D 214 HIS D 262 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100252 restraints weight = 14223.703| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.86 r_work: 0.3115 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9436 Z= 0.196 Angle : 0.654 9.672 12834 Z= 0.314 Chirality : 0.044 0.159 1536 Planarity : 0.005 0.098 1606 Dihedral : 10.309 86.727 1428 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 7.75 % Allowed : 19.11 % Favored : 73.14 % 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: -2.80 (0.23), residues: 1202 helix: -1.30 (0.19), residues: 658 sheet: -1.77 (0.56), residues: 94 loop : -2.58 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 7 HIS 0.005 0.001 HIS C 62 PHE 0.009 0.001 PHE D 91 TYR 0.015 0.001 TYR C 81 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8611 (mt) REVERT: A 96 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8590 (tp) REVERT: A 116 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7318 (mp) REVERT: A 120 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8031 (pt) REVERT: A 143 VAL cc_start: 0.9244 (t) cc_final: 0.8927 (p) REVERT: A 216 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 31 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 56 MET cc_start: 0.8456 (tpp) cc_final: 0.8244 (tpp) REVERT: B 70 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 96 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8475 (tt) REVERT: B 120 ILE cc_start: 0.8668 (pt) cc_final: 0.8105 (pt) REVERT: B 123 MET cc_start: 0.8352 (mtt) cc_final: 0.8150 (mtm) REVERT: B 143 VAL cc_start: 0.9226 (t) cc_final: 0.8907 (p) REVERT: C 105 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: C 170 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 172 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8127 (p90) REVERT: D 105 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7844 (m-40) REVERT: D 172 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8257 (p90) REVERT: D 249 ASP cc_start: 0.8203 (t0) cc_final: 0.7510 (p0) REVERT: E 22 GLN cc_start: 0.8296 (pp30) cc_final: 0.7760 (mp10) REVERT: E 66 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8326 (tppt) REVERT: E 89 ASN cc_start: 0.8793 (t0) cc_final: 0.8065 (t0) REVERT: F 7 TRP cc_start: 0.8220 (p90) cc_final: 0.7524 (p-90) REVERT: F 22 GLN cc_start: 0.8291 (pp30) cc_final: 0.7893 (mp10) REVERT: F 23 ASP cc_start: 0.8566 (t0) cc_final: 0.8008 (t0) REVERT: F 66 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8435 (mmtt) REVERT: F 68 GLN cc_start: 0.8409 (pp30) cc_final: 0.8092 (pm20) REVERT: F 89 ASN cc_start: 0.8798 (t0) cc_final: 0.8269 (t0) outliers start: 77 outliers final: 42 residues processed: 277 average time/residue: 0.2016 time to fit residues: 78.4625 Evaluate side-chains 245 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 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 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 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 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 220 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 262 HIS D 214 HIS D 262 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101190 restraints weight = 13621.736| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.96 r_work: 0.3092 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9436 Z= 0.226 Angle : 0.658 12.242 12834 Z= 0.315 Chirality : 0.044 0.144 1536 Planarity : 0.006 0.103 1606 Dihedral : 9.782 89.905 1416 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 8.25 % Allowed : 19.32 % Favored : 72.43 % 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: -2.42 (0.23), residues: 1202 helix: -1.02 (0.19), residues: 662 sheet: -1.58 (0.55), residues: 94 loop : -2.37 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 7 HIS 0.005 0.001 HIS D 62 PHE 0.012 0.001 PHE B 162 TYR 0.013 0.001 TYR C 81 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 216 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 98 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7502 (tt0) REVERT: A 116 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 120 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8226 (pt) REVERT: A 133 GLU cc_start: 0.8531 (tt0) cc_final: 0.8292 (tt0) REVERT: A 216 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 31 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 56 MET cc_start: 0.8515 (tpp) cc_final: 0.8280 (tpp) REVERT: B 84 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6999 (pp20) REVERT: B 96 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8455 (tt) REVERT: B 120 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8141 (pt) REVERT: B 123 MET cc_start: 0.8301 (mtt) cc_final: 0.8091 (mtm) REVERT: B 132 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8335 (ttm) REVERT: B 134 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8165 (tpp) REVERT: C 51 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 105 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7955 (m-40) REVERT: C 143 SER cc_start: 0.8680 (t) cc_final: 0.8462 (p) REVERT: C 172 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7895 (p90) REVERT: D 105 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7886 (m110) REVERT: D 143 SER cc_start: 0.8712 (t) cc_final: 0.8483 (p) REVERT: D 172 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8022 (p90) REVERT: D 249 ASP cc_start: 0.8214 (t0) cc_final: 0.7423 (p0) REVERT: E 66 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8330 (tptt) REVERT: E 89 ASN cc_start: 0.8777 (t0) cc_final: 0.7953 (t0) REVERT: F 7 TRP cc_start: 0.8220 (p90) cc_final: 0.7655 (p-90) REVERT: F 23 ASP cc_start: 0.8554 (t0) cc_final: 0.8285 (t0) REVERT: F 68 GLN cc_start: 0.8389 (pp30) cc_final: 0.8087 (pm20) REVERT: F 89 ASN cc_start: 0.8737 (t0) cc_final: 0.8114 (t0) outliers start: 82 outliers final: 53 residues processed: 281 average time/residue: 0.1953 time to fit residues: 77.1752 Evaluate side-chains 269 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 120 ILE 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 120 ILE Chi-restraints excluded: chain B residue 132 MET 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 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.0020 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 220 ASN C 71 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101929 restraints weight = 13565.085| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.97 r_work: 0.3106 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3252 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= 0.217 Angle : 0.626 9.662 12834 Z= 0.305 Chirality : 0.043 0.143 1536 Planarity : 0.005 0.100 1606 Dihedral : 9.623 84.303 1414 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 8.45 % Allowed : 20.22 % 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: -2.20 (0.24), residues: 1202 helix: -0.81 (0.19), residues: 664 sheet: -1.58 (0.54), residues: 94 loop : -2.29 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 7 HIS 0.007 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.010 0.001 TYR C 81 ARG 0.006 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 211 time to evaluate : 1.029 Fit side-chains REVERT: A 31 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8564 (mt) REVERT: A 98 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7596 (tt0) REVERT: A 116 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7516 (mp) REVERT: A 128 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: A 133 GLU cc_start: 0.8521 (tt0) cc_final: 0.8256 (tt0) REVERT: A 197 MET cc_start: 0.7022 (tpp) cc_final: 0.6747 (tpp) REVERT: A 216 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8302 (mm) REVERT: A 257 MET cc_start: 0.7984 (mtm) cc_final: 0.7747 (mtm) REVERT: B 31 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 56 MET cc_start: 0.8518 (tpp) cc_final: 0.8275 (tpp) REVERT: B 96 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 120 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8061 (pt) REVERT: B 123 MET cc_start: 0.8328 (mtt) cc_final: 0.8111 (mtm) REVERT: B 134 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8548 (tpp) REVERT: C 51 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 105 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7902 (m110) REVERT: C 143 SER cc_start: 0.8623 (t) cc_final: 0.8414 (p) REVERT: C 172 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7880 (p90) REVERT: D 105 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7997 (m110) REVERT: D 143 SER cc_start: 0.8672 (t) cc_final: 0.8458 (p) REVERT: D 172 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7959 (p90) REVERT: D 249 ASP cc_start: 0.8239 (t0) cc_final: 0.7496 (p0) REVERT: E 22 GLN cc_start: 0.8286 (pp30) cc_final: 0.7876 (mp10) REVERT: E 66 LYS cc_start: 0.8574 (mmtm) cc_final: 0.8342 (tptt) REVERT: E 89 ASN cc_start: 0.8797 (t0) cc_final: 0.7944 (t0) REVERT: F 7 TRP cc_start: 0.8195 (p90) cc_final: 0.7614 (p-90) REVERT: F 22 GLN cc_start: 0.8347 (pp30) cc_final: 0.7894 (mp10) REVERT: F 23 ASP cc_start: 0.8575 (t0) cc_final: 0.8034 (t0) REVERT: F 66 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8313 (tppt) REVERT: F 68 GLN cc_start: 0.8299 (pp30) cc_final: 0.8059 (pm20) REVERT: F 89 ASN cc_start: 0.8757 (t0) cc_final: 0.8104 (t0) outliers start: 84 outliers final: 52 residues processed: 279 average time/residue: 0.2028 time to fit residues: 78.7363 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 : 1.058 ------------------------------------------------------------------------------- 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 128 GLN Chi-restraints excluded: chain A residue 134 MET 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 120 ILE 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 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN ** D 113 HIS ** 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 = 0.3529 r_free = 0.3529 target = 0.121732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099718 restraints weight = 14026.261| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.84 r_work: 0.3108 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9436 Z= 0.231 Angle : 0.639 9.728 12834 Z= 0.310 Chirality : 0.044 0.169 1536 Planarity : 0.005 0.098 1606 Dihedral : 9.394 88.957 1409 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 7.44 % Allowed : 21.43 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1202 helix: -0.62 (0.20), residues: 658 sheet: -1.62 (0.53), residues: 94 loop : -2.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 195 HIS 0.004 0.001 HIS C 113 PHE 0.013 0.001 PHE B 162 TYR 0.006 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 211 time to evaluate : 0.942 Fit side-chains REVERT: A 31 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8550 (mt) REVERT: A 98 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7590 (tt0) REVERT: A 116 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 120 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8176 (pt) REVERT: A 128 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 133 GLU cc_start: 0.8453 (tt0) cc_final: 0.8211 (tt0) REVERT: A 201 ASN cc_start: 0.7453 (m-40) cc_final: 0.7221 (m-40) REVERT: A 216 ILE cc_start: 0.8734 (pp) cc_final: 0.8348 (mm) REVERT: B 31 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 56 MET cc_start: 0.8457 (tpp) cc_final: 0.8219 (tpp) REVERT: B 96 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8298 (tt) REVERT: B 120 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8150 (pt) REVERT: B 123 MET cc_start: 0.8409 (mtt) cc_final: 0.8178 (mtm) REVERT: B 134 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8605 (tpp) REVERT: B 191 ASN cc_start: 0.7346 (m-40) cc_final: 0.6972 (p0) REVERT: B 198 ASP cc_start: 0.8155 (t0) cc_final: 0.7815 (t0) REVERT: C 105 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.8019 (m110) REVERT: C 143 SER cc_start: 0.8594 (t) cc_final: 0.8383 (p) REVERT: C 207 GLU cc_start: 0.8197 (mp0) cc_final: 0.7923 (mp0) REVERT: C 262 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6876 (m-70) REVERT: D 105 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8115 (m110) REVERT: D 143 SER cc_start: 0.8543 (t) cc_final: 0.8341 (p) REVERT: D 172 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7988 (p90) REVERT: D 249 ASP cc_start: 0.8177 (t0) cc_final: 0.7584 (p0) REVERT: E 7 TRP cc_start: 0.8220 (p90) cc_final: 0.7742 (p-90) REVERT: E 22 GLN cc_start: 0.8274 (pp30) cc_final: 0.7863 (mp10) REVERT: E 66 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8280 (tptt) REVERT: E 89 ASN cc_start: 0.8827 (t0) cc_final: 0.7953 (t0) REVERT: F 7 TRP cc_start: 0.8252 (p90) cc_final: 0.7562 (p-90) REVERT: F 23 ASP cc_start: 0.8556 (t0) cc_final: 0.8270 (t0) REVERT: F 66 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8267 (tppt) REVERT: F 68 GLN cc_start: 0.8188 (pp30) cc_final: 0.7979 (pm20) REVERT: F 89 ASN cc_start: 0.8820 (t0) cc_final: 0.8183 (t0) outliers start: 74 outliers final: 51 residues processed: 271 average time/residue: 0.2169 time to fit residues: 80.9685 Evaluate side-chains 266 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 134 MET 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 120 ILE 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 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 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 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 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 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 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: 4.9990 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** 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 = 0.3562 r_free = 0.3562 target = 0.126256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103588 restraints weight = 13527.464| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.3131 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3546 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= 0.196 Angle : 0.631 11.423 12834 Z= 0.304 Chirality : 0.043 0.147 1536 Planarity : 0.005 0.094 1606 Dihedral : 9.117 84.909 1408 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.65 % Allowed : 21.43 % 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: -1.73 (0.24), residues: 1202 helix: -0.37 (0.20), residues: 652 sheet: -1.36 (0.57), residues: 84 loop : -2.16 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 7 HIS 0.005 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.003 0.001 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 216 time to evaluate : 0.973 Fit side-chains REVERT: A 31 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 98 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7554 (tt0) REVERT: A 116 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 133 GLU cc_start: 0.8487 (tt0) cc_final: 0.8266 (tt0) REVERT: A 197 MET cc_start: 0.7075 (tpp) cc_final: 0.6601 (tpp) REVERT: A 216 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8402 (mm) REVERT: B 31 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 56 MET cc_start: 0.8472 (tpp) cc_final: 0.8214 (tpp) REVERT: B 73 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: B 96 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B 123 MET cc_start: 0.8314 (mtt) cc_final: 0.8082 (mtm) REVERT: B 134 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8495 (tpp) REVERT: B 191 ASN cc_start: 0.7397 (m-40) cc_final: 0.7009 (p0) REVERT: B 198 ASP cc_start: 0.8206 (t0) cc_final: 0.7789 (t0) REVERT: B 201 ASN cc_start: 0.8108 (m-40) cc_final: 0.7892 (m-40) REVERT: C 51 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8295 (mp) REVERT: C 105 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8070 (m110) REVERT: C 207 GLU cc_start: 0.8206 (mp0) cc_final: 0.7951 (mp0) REVERT: C 235 ASN cc_start: 0.8312 (t0) cc_final: 0.8044 (t0) REVERT: C 262 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6965 (m-70) REVERT: D 172 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7878 (p90) REVERT: D 249 ASP cc_start: 0.8139 (t0) cc_final: 0.7502 (p0) REVERT: E 7 TRP cc_start: 0.8237 (p90) cc_final: 0.7765 (p-90) REVERT: E 22 GLN cc_start: 0.8173 (pp30) cc_final: 0.7881 (mp10) REVERT: E 66 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8286 (tptt) REVERT: E 89 ASN cc_start: 0.8802 (t0) cc_final: 0.8182 (t0) REVERT: F 7 TRP cc_start: 0.8227 (p90) cc_final: 0.7509 (p-90) REVERT: F 22 GLN cc_start: 0.8214 (pp30) cc_final: 0.7868 (mp10) REVERT: F 23 ASP cc_start: 0.8549 (t0) cc_final: 0.8022 (t0) REVERT: F 66 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8218 (tppt) REVERT: F 89 ASN cc_start: 0.8799 (t0) cc_final: 0.8169 (t0) outliers start: 76 outliers final: 56 residues processed: 277 average time/residue: 0.2149 time to fit residues: 81.9854 Evaluate side-chains 265 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 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 134 MET 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 134 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain 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 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 84 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN D 105 ASN D 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104571 restraints weight = 13655.074| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.94 r_work: 0.3147 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3664 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= 0.197 Angle : 0.636 10.198 12834 Z= 0.305 Chirality : 0.043 0.147 1536 Planarity : 0.005 0.093 1606 Dihedral : 8.576 74.363 1405 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.55 % Allowed : 22.03 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1202 helix: -0.18 (0.20), residues: 646 sheet: -1.25 (0.58), residues: 84 loop : -1.98 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 7 HIS 0.003 0.001 HIS D 62 PHE 0.012 0.001 PHE B 162 TYR 0.004 0.001 TYR D 81 ARG 0.007 0.000 ARG D 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 208 time to evaluate : 0.991 Fit side-chains REVERT: A 31 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 98 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7522 (tt0) REVERT: A 116 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 120 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8036 (pt) REVERT: A 128 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: A 133 GLU cc_start: 0.8485 (tt0) cc_final: 0.8270 (tt0) REVERT: A 134 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8610 (tpp) REVERT: A 216 ILE cc_start: 0.8687 (pp) cc_final: 0.8348 (mm) REVERT: B 31 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8628 (mt) REVERT: B 56 MET cc_start: 0.8448 (tpp) cc_final: 0.8185 (tpp) REVERT: B 73 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: B 96 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 98 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7457 (tt0) REVERT: B 123 MET cc_start: 0.8312 (mtt) cc_final: 0.8084 (mtm) REVERT: B 134 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: B 191 ASN cc_start: 0.7384 (m-40) cc_final: 0.6994 (p0) REVERT: B 198 ASP cc_start: 0.8192 (t0) cc_final: 0.7775 (t0) REVERT: B 201 ASN cc_start: 0.8030 (m-40) cc_final: 0.7745 (m-40) REVERT: C 51 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 75 MET cc_start: 0.7990 (mtt) cc_final: 0.7719 (mtt) REVERT: C 207 GLU cc_start: 0.8182 (mp0) cc_final: 0.7916 (mp0) REVERT: C 235 ASN cc_start: 0.8260 (t0) cc_final: 0.8023 (t0) REVERT: C 262 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6974 (m-70) REVERT: D 172 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.7870 (p90) REVERT: D 249 ASP cc_start: 0.8218 (t0) cc_final: 0.7551 (p0) REVERT: E 7 TRP cc_start: 0.8230 (p90) cc_final: 0.7815 (p-90) REVERT: E 22 GLN cc_start: 0.8164 (pp30) cc_final: 0.7831 (mp10) REVERT: E 66 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8248 (tptt) REVERT: E 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8127 (t0) REVERT: F 7 TRP cc_start: 0.8214 (p90) cc_final: 0.7510 (p-90) REVERT: F 33 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8591 (mm-30) REVERT: F 66 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8118 (tppt) REVERT: F 89 ASN cc_start: 0.8840 (t0) cc_final: 0.8223 (t0) outliers start: 75 outliers final: 53 residues processed: 268 average time/residue: 0.2141 time to fit residues: 79.1161 Evaluate side-chains 265 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 134 MET 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 94 SER Chi-restraints excluded: chain B residue 96 LEU 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 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain 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 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 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 44 LEU Chi-restraints excluded: chain E residue 47 VAL 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 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: 1.9990 chunk 1 optimal weight: 0.0170 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 97 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 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 = 0.3597 r_free = 0.3597 target = 0.128813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106554 restraints weight = 13419.231| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.93 r_work: 0.3177 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9436 Z= 0.184 Angle : 0.633 9.565 12834 Z= 0.305 Chirality : 0.042 0.161 1536 Planarity : 0.005 0.089 1606 Dihedral : 7.988 60.019 1401 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.64 % Allowed : 23.34 % 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: -1.31 (0.25), residues: 1202 helix: -0.04 (0.20), residues: 660 sheet: -1.13 (0.59), residues: 84 loop : -1.98 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 7 HIS 0.003 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.004 0.001 TYR F 88 ARG 0.006 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 0.998 Fit side-chains REVERT: A 31 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 98 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7515 (tt0) REVERT: A 116 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 133 GLU cc_start: 0.8480 (tt0) cc_final: 0.8259 (tt0) REVERT: A 134 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8549 (tpp) REVERT: A 201 ASN cc_start: 0.7978 (m-40) cc_final: 0.7778 (m-40) REVERT: A 216 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8334 (mm) REVERT: B 56 MET cc_start: 0.8399 (tpp) cc_final: 0.8120 (tpp) REVERT: B 96 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 98 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7441 (tt0) REVERT: B 120 ILE cc_start: 0.8588 (pt) cc_final: 0.8093 (pt) REVERT: B 134 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8347 (tpp) REVERT: B 191 ASN cc_start: 0.7373 (m-40) cc_final: 0.7008 (p0) REVERT: B 198 ASP cc_start: 0.8211 (t0) cc_final: 0.7801 (t0) REVERT: B 201 ASN cc_start: 0.7959 (m-40) cc_final: 0.7636 (m-40) REVERT: C 51 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 75 MET cc_start: 0.7930 (mtt) cc_final: 0.7698 (mtt) REVERT: C 207 GLU cc_start: 0.8154 (mp0) cc_final: 0.7919 (mp0) REVERT: D 12 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7818 (mmt90) REVERT: D 83 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8964 (p) REVERT: D 249 ASP cc_start: 0.8147 (t0) cc_final: 0.7553 (p0) REVERT: D 252 VAL cc_start: 0.8782 (t) cc_final: 0.8493 (p) REVERT: E 7 TRP cc_start: 0.8157 (p90) cc_final: 0.7763 (p-90) REVERT: E 66 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8216 (tptt) REVERT: E 89 ASN cc_start: 0.8768 (t0) cc_final: 0.8085 (t0) REVERT: F 7 TRP cc_start: 0.8199 (p90) cc_final: 0.7534 (p-90) REVERT: F 33 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8578 (mm-30) REVERT: F 66 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8048 (tppt) REVERT: F 89 ASN cc_start: 0.8840 (t0) cc_final: 0.8231 (t0) outliers start: 66 outliers final: 53 residues processed: 264 average time/residue: 0.2183 time to fit residues: 79.6207 Evaluate side-chains 261 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 134 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 LEU 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 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain 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 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 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 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN C 175 GLN ** 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 = 0.3575 r_free = 0.3575 target = 0.127008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104481 restraints weight = 13646.580| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.94 r_work: 0.3147 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9436 Z= 0.222 Angle : 0.651 9.647 12834 Z= 0.313 Chirality : 0.043 0.156 1536 Planarity : 0.005 0.090 1606 Dihedral : 7.810 58.954 1397 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.54 % Allowed : 24.35 % Favored : 69.11 % 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: -1.25 (0.25), residues: 1202 helix: 0.02 (0.20), residues: 658 sheet: -1.06 (0.59), residues: 84 loop : -1.98 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 7 HIS 0.002 0.001 HIS D 62 PHE 0.013 0.001 PHE B 162 TYR 0.005 0.001 TYR B 75 ARG 0.007 0.000 ARG D 12 ********************** 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 267 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 202 time to evaluate : 1.027 Fit side-chains REVERT: A 31 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 98 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7641 (tt0) REVERT: A 116 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7438 (mp) REVERT: A 128 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 133 GLU cc_start: 0.8526 (tt0) cc_final: 0.8293 (tt0) REVERT: A 134 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8632 (tpp) REVERT: A 201 ASN cc_start: 0.8027 (m-40) cc_final: 0.7737 (m-40) REVERT: A 216 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8328 (mm) REVERT: B 56 MET cc_start: 0.8377 (tpp) cc_final: 0.8108 (tpp) REVERT: B 73 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: B 96 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8256 (tt) REVERT: B 98 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7551 (tt0) REVERT: B 120 ILE cc_start: 0.8686 (pt) cc_final: 0.8196 (pt) REVERT: B 134 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8473 (tpp) REVERT: B 191 ASN cc_start: 0.7403 (m-40) cc_final: 0.7029 (p0) REVERT: B 198 ASP cc_start: 0.8209 (t0) cc_final: 0.7770 (t0) REVERT: B 201 ASN cc_start: 0.8101 (m-40) cc_final: 0.7869 (m-40) REVERT: C 51 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 75 MET cc_start: 0.7836 (mtt) cc_final: 0.7600 (mtt) REVERT: C 207 GLU cc_start: 0.8185 (mp0) cc_final: 0.7948 (mp0) REVERT: D 12 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7872 (mmt90) REVERT: D 83 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8968 (p) REVERT: D 249 ASP cc_start: 0.8136 (t0) cc_final: 0.7552 (p0) REVERT: E 7 TRP cc_start: 0.8221 (p90) cc_final: 0.7759 (p-90) REVERT: E 66 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8209 (tptt) REVERT: F 7 TRP cc_start: 0.8222 (p90) cc_final: 0.7526 (p-90) REVERT: F 33 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8604 (mm-30) REVERT: F 66 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8057 (tppt) REVERT: F 89 ASN cc_start: 0.8791 (t0) cc_final: 0.8145 (t0) outliers start: 65 outliers final: 52 residues processed: 253 average time/residue: 0.2167 time to fit residues: 75.3319 Evaluate side-chains 260 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 128 GLN Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR 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 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 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 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.0170 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3593 r_free = 0.3593 target = 0.128409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105947 restraints weight = 13419.799| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.93 r_work: 0.3166 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3938 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= 0.197 Angle : 0.640 9.647 12834 Z= 0.307 Chirality : 0.043 0.152 1536 Planarity : 0.005 0.086 1606 Dihedral : 7.665 57.986 1397 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.84 % Allowed : 24.14 % Favored : 69.01 % 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: -1.11 (0.25), residues: 1202 helix: 0.12 (0.21), residues: 656 sheet: -0.88 (0.60), residues: 84 loop : -1.92 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 7 HIS 0.003 0.001 HIS D 62 PHE 0.013 0.001 PHE B 162 TYR 0.004 0.001 TYR B 75 ARG 0.007 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4600.40 seconds wall clock time: 82 minutes 15.26 seconds (4935.26 seconds total)