Starting phenix.real_space_refine on Thu Mar 5 09:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qcz_4514/03_2026/6qcz_4514.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qcz_4514/03_2026/6qcz_4514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qcz_4514/03_2026/6qcz_4514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qcz_4514/03_2026/6qcz_4514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qcz_4514/03_2026/6qcz_4514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qcz_4514/03_2026/6qcz_4514.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 44 5.16 5 C 6936 2.51 5 N 1820 2.21 5 O 1844 1.98 5 H 11100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "D" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.18 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 102.7, 94.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 44 16.00 O 1844 8.00 N 1820 7.00 C 6936 6.00 H 11100 1.00 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: 2.02 Conformation dependent library (CDL) restraints added in 539.5 milliseconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 65.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.597A pdb=" N ILE A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 3.576A pdb=" N ARG A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.557A pdb=" N ILE A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 4.027A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.222A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.614A pdb=" N ALA A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 225 removed outlier: 3.752A pdb=" N ARG A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.901A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.597A pdb=" N ILE B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.577A pdb=" N ARG B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 92 removed outlier: 4.556A pdb=" N ILE B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 4.027A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.223A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.613A pdb=" N ALA B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 225 removed outlier: 3.752A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.899A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.596A pdb=" N ILE C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 61 removed outlier: 3.577A pdb=" N ARG C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 4.557A pdb=" N ILE C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 4.027A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.222A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.613A pdb=" N ALA C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 225 removed outlier: 3.753A pdb=" N ARG C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.901A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.597A pdb=" N ILE D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.577A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 removed outlier: 4.557A pdb=" N ILE D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 4.027A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.223A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 161 through 174 removed outlier: 3.613A pdb=" N ALA D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 225 removed outlier: 3.752A pdb=" N ARG D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU D 244 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.900A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 256 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA4, first strand: chain 'B' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AA6, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA8, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AA9, first strand: chain 'C' and resid 294 through 296 Processing sheet with id=AB1, first strand: chain 'D' and resid 253 through 256 Processing sheet with id=AB2, first strand: chain 'D' and resid 261 through 263 Processing sheet with id=AB3, first strand: chain 'D' and resid 294 through 296 520 hydrogen bonds defined for protein. 1416 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: 4.65 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 11088 1.02 - 1.22: 16 1.22 - 1.42: 4369 1.42 - 1.62: 6431 1.62 - 1.81: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" N GLU D 305 " pdb=" CA GLU D 305 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.41e-02 5.03e+03 5.03e+00 bond pdb=" N GLU A 305 " pdb=" CA GLU A 305 " ideal model delta sigma weight residual 1.457 1.425 0.031 1.41e-02 5.03e+03 4.96e+00 bond pdb=" N GLU C 305 " pdb=" CA GLU C 305 " ideal model delta sigma weight residual 1.457 1.426 0.031 1.41e-02 5.03e+03 4.79e+00 bond pdb=" N GLU B 305 " pdb=" CA GLU B 305 " ideal model delta sigma weight residual 1.457 1.426 0.031 1.41e-02 5.03e+03 4.71e+00 bond pdb=" CG1 ILE D 30 " pdb=" CD1 ILE D 30 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 4.03e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 35436 1.41 - 2.82: 3854 2.82 - 4.23: 499 4.23 - 5.64: 130 5.64 - 7.06: 21 Bond angle restraints: 39940 Sorted by residual: angle pdb=" N ASN D 124 " pdb=" CA ASN D 124 " pdb=" C ASN D 124 " ideal model delta sigma weight residual 114.04 109.21 4.83 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N ASN C 124 " pdb=" CA ASN C 124 " pdb=" C ASN C 124 " ideal model delta sigma weight residual 114.04 109.22 4.82 1.24e+00 6.50e-01 1.51e+01 angle pdb=" N ASN B 124 " pdb=" CA ASN B 124 " pdb=" C ASN B 124 " ideal model delta sigma weight residual 114.04 109.24 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" N ASN A 124 " pdb=" CA ASN A 124 " pdb=" C ASN A 124 " ideal model delta sigma weight residual 114.04 109.25 4.79 1.24e+00 6.50e-01 1.49e+01 angle pdb=" N ALA A 294 " pdb=" CA ALA A 294 " pdb=" C ALA A 294 " ideal model delta sigma weight residual 108.86 113.28 -4.42 1.41e+00 5.03e-01 9.83e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 9280 14.92 - 29.83: 685 29.83 - 44.75: 199 44.75 - 59.67: 116 59.67 - 74.59: 8 Dihedral angle restraints: 10288 sinusoidal: 5604 harmonic: 4684 Sorted by residual: dihedral pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N ALA A 26 " pdb=" CA ALA A 26 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL C 25 " pdb=" C VAL C 25 " pdb=" N ALA C 26 " pdb=" CA ALA C 26 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA VAL D 25 " pdb=" C VAL D 25 " pdb=" N ALA D 26 " pdb=" CA ALA D 26 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 10285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 957 0.031 - 0.062: 496 0.062 - 0.093: 219 0.093 - 0.124: 92 0.124 - 0.156: 20 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CG LEU A 106 " pdb=" CB LEU A 106 " pdb=" CD1 LEU A 106 " pdb=" CD2 LEU A 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CG LEU C 106 " pdb=" CB LEU C 106 " pdb=" CD1 LEU C 106 " pdb=" CD2 LEU C 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CG LEU D 106 " pdb=" CB LEU D 106 " pdb=" CD1 LEU D 106 " pdb=" CD2 LEU D 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 176 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C THR D 176 " -0.034 2.00e-02 2.50e+03 pdb=" O THR D 176 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY D 177 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 176 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C THR A 176 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A 176 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 177 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 176 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C THR C 176 " 0.033 2.00e-02 2.50e+03 pdb=" O THR C 176 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 177 " -0.011 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.32: 5967 2.32 - 3.03: 62504 3.03 - 3.73: 74299 3.73 - 4.44: 114856 4.44 - 5.14: 175144 Nonbonded interactions: 432770 Sorted by model distance: nonbonded pdb=" O LYS D 74 " pdb=" HE ARG D 110 " model vdw 1.618 2.450 nonbonded pdb=" O LYS A 74 " pdb=" HE ARG A 110 " model vdw 1.618 2.450 nonbonded pdb=" O LYS C 74 " pdb=" HE ARG C 110 " model vdw 1.619 2.450 nonbonded pdb=" O LYS B 74 " pdb=" HE ARG B 110 " model vdw 1.619 2.450 nonbonded pdb=" H GLY A 259 " pdb=" O ALA A 313 " model vdw 1.651 2.450 ... (remaining 432765 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 0.070 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: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 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 : 0.009 0.078 10880 Z= 0.426 Angle : 1.002 7.056 14852 Z= 0.558 Chirality : 0.048 0.156 1784 Planarity : 0.006 0.039 1872 Dihedral : 9.452 74.586 3844 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.21), residues: 1412 helix: -3.45 (0.15), residues: 592 sheet: -3.55 (0.60), residues: 40 loop : -2.13 (0.25), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 220 TYR 0.023 0.005 TYR C 178 PHE 0.018 0.003 PHE D 141 TRP 0.015 0.003 TRP D 227 HIS 0.005 0.003 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00899 (10880) covalent geometry : angle 1.00215 (14852) hydrogen bonds : bond 0.33311 ( 520) hydrogen bonds : angle 11.84652 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8133 (mt0) cc_final: 0.7873 (mt0) REVERT: A 247 ILE cc_start: 0.8980 (mt) cc_final: 0.8668 (tp) REVERT: A 272 MET cc_start: 0.6080 (ptm) cc_final: 0.5817 (ptm) REVERT: A 327 PHE cc_start: 0.7039 (t80) cc_final: 0.6571 (t80) REVERT: A 346 LEU cc_start: 0.8351 (mt) cc_final: 0.8142 (tt) REVERT: B 155 GLN cc_start: 0.8145 (mt0) cc_final: 0.7848 (mt0) REVERT: B 327 PHE cc_start: 0.7138 (t80) cc_final: 0.6650 (t80) REVERT: B 346 LEU cc_start: 0.8372 (mt) cc_final: 0.8115 (tt) REVERT: C 155 GLN cc_start: 0.7830 (mt0) cc_final: 0.7531 (mt0) REVERT: C 247 ILE cc_start: 0.8905 (mt) cc_final: 0.8676 (tp) REVERT: C 327 PHE cc_start: 0.7141 (t80) cc_final: 0.6643 (t80) REVERT: C 346 LEU cc_start: 0.8369 (mt) cc_final: 0.8089 (tt) REVERT: D 155 GLN cc_start: 0.8100 (mt0) cc_final: 0.7688 (mt0) REVERT: D 247 ILE cc_start: 0.8967 (mt) cc_final: 0.8656 (tp) REVERT: D 327 PHE cc_start: 0.7136 (t80) cc_final: 0.6664 (t80) REVERT: D 346 LEU cc_start: 0.8277 (mt) cc_final: 0.7954 (tt) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2312 time to fit residues: 144.5862 Evaluate side-chains 346 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.229146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188249 restraints weight = 60013.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.194264 restraints weight = 34140.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.198077 restraints weight = 22766.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.200501 restraints weight = 17188.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.201997 restraints weight = 14271.527| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10880 Z= 0.182 Angle : 0.723 8.131 14852 Z= 0.383 Chirality : 0.042 0.141 1784 Planarity : 0.007 0.058 1872 Dihedral : 6.703 26.285 1536 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.09 % Allowed : 1.47 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.20), residues: 1412 helix: -2.78 (0.15), residues: 696 sheet: -3.27 (0.61), residues: 40 loop : -2.46 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 252 TYR 0.011 0.002 TYR D 52 PHE 0.025 0.002 PHE B 214 TRP 0.008 0.001 TRP D 168 HIS 0.001 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00352 (10880) covalent geometry : angle 0.72322 (14852) hydrogen bonds : bond 0.07820 ( 520) hydrogen bonds : angle 7.45189 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.5700 (ptm) cc_final: 0.5470 (ptm) REVERT: A 327 PHE cc_start: 0.6739 (t80) cc_final: 0.6459 (t80) REVERT: A 346 LEU cc_start: 0.8292 (mt) cc_final: 0.7962 (tt) REVERT: B 197 MET cc_start: 0.7874 (ttm) cc_final: 0.7634 (ttm) REVERT: B 327 PHE cc_start: 0.6853 (t80) cc_final: 0.6463 (t80) REVERT: B 346 LEU cc_start: 0.8187 (mt) cc_final: 0.7964 (tt) REVERT: C 170 VAL cc_start: 0.8284 (m) cc_final: 0.7847 (p) REVERT: C 327 PHE cc_start: 0.6890 (t80) cc_final: 0.6430 (t80) REVERT: C 346 LEU cc_start: 0.8132 (mt) cc_final: 0.7899 (tt) REVERT: D 155 GLN cc_start: 0.7633 (mt0) cc_final: 0.7232 (mt0) REVERT: D 243 VAL cc_start: 0.9187 (t) cc_final: 0.8842 (t) REVERT: D 346 LEU cc_start: 0.8025 (mt) cc_final: 0.7752 (tt) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.1906 time to fit residues: 106.6254 Evaluate side-chains 323 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 40.0000 chunk 80 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4625 r_free = 0.4625 target = 0.224394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.184409 restraints weight = 59814.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.190226 restraints weight = 33486.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.193950 restraints weight = 22289.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.196287 restraints weight = 16808.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.197693 restraints weight = 13929.146| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10880 Z= 0.197 Angle : 0.678 6.457 14852 Z= 0.364 Chirality : 0.041 0.161 1784 Planarity : 0.005 0.052 1872 Dihedral : 6.268 21.643 1536 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.20), residues: 1412 helix: -2.16 (0.17), residues: 704 sheet: -3.39 (0.63), residues: 40 loop : -2.71 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 252 TYR 0.011 0.002 TYR C 178 PHE 0.022 0.002 PHE B 214 TRP 0.031 0.001 TRP C 167 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00378 (10880) covalent geometry : angle 0.67803 (14852) hydrogen bonds : bond 0.06298 ( 520) hydrogen bonds : angle 6.64629 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.8147 (mt0) cc_final: 0.7307 (mp10) REVERT: A 272 MET cc_start: 0.5759 (ptm) cc_final: 0.5521 (ptm) REVERT: A 346 LEU cc_start: 0.8241 (mt) cc_final: 0.7952 (tt) REVERT: B 247 ILE cc_start: 0.9036 (pt) cc_final: 0.8519 (tp) REVERT: B 346 LEU cc_start: 0.8192 (mt) cc_final: 0.7947 (tt) REVERT: C 217 GLU cc_start: 0.8008 (tp30) cc_final: 0.7782 (tp30) REVERT: C 346 LEU cc_start: 0.8151 (mt) cc_final: 0.7917 (tt) REVERT: D 155 GLN cc_start: 0.7224 (mt0) cc_final: 0.6734 (mt0) REVERT: D 346 LEU cc_start: 0.8133 (mt) cc_final: 0.7889 (tt) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1847 time to fit residues: 102.5115 Evaluate side-chains 322 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4615 r_free = 0.4615 target = 0.223714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.183162 restraints weight = 59860.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.188391 restraints weight = 35200.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191496 restraints weight = 24296.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.193687 restraints weight = 19241.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.194859 restraints weight = 16363.961| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10880 Z= 0.167 Angle : 0.631 5.287 14852 Z= 0.336 Chirality : 0.040 0.135 1784 Planarity : 0.005 0.038 1872 Dihedral : 5.774 20.043 1536 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.20), residues: 1412 helix: -1.79 (0.18), residues: 712 sheet: -3.33 (0.65), residues: 40 loop : -2.71 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.010 0.002 TYR C 178 PHE 0.018 0.002 PHE B 214 TRP 0.017 0.002 TRP A 206 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00328 (10880) covalent geometry : angle 0.63051 (14852) hydrogen bonds : bond 0.05132 ( 520) hydrogen bonds : angle 6.02431 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.3497 (ptt) cc_final: -0.3797 (ptt) REVERT: A 33 MET cc_start: 0.6546 (tpt) cc_final: 0.6188 (tpt) REVERT: A 346 LEU cc_start: 0.8252 (mt) cc_final: 0.7971 (tt) REVERT: B 78 ASP cc_start: 0.7596 (m-30) cc_final: 0.7323 (m-30) REVERT: B 247 ILE cc_start: 0.8995 (pt) cc_final: 0.8500 (tp) REVERT: B 307 ARG cc_start: 0.6015 (mmm160) cc_final: 0.5763 (mmm160) REVERT: B 346 LEU cc_start: 0.8117 (mt) cc_final: 0.7890 (tt) REVERT: C 217 GLU cc_start: 0.8024 (tp30) cc_final: 0.7772 (tp30) REVERT: C 346 LEU cc_start: 0.8248 (mt) cc_final: 0.8007 (tt) REVERT: D 78 ASP cc_start: 0.7617 (m-30) cc_final: 0.7335 (m-30) REVERT: D 155 GLN cc_start: 0.7204 (mt0) cc_final: 0.6760 (mt0) REVERT: D 164 GLN cc_start: 0.6360 (mp10) cc_final: 0.5755 (mp10) REVERT: D 189 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.8010 (mtt180) REVERT: D 197 MET cc_start: 0.8668 (tpp) cc_final: 0.7848 (tpp) REVERT: D 346 LEU cc_start: 0.8176 (mt) cc_final: 0.7931 (tt) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1793 time to fit residues: 102.9186 Evaluate side-chains 330 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 0.0270 chunk 16 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 135 optimal weight: 50.0000 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.222732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.182313 restraints weight = 59428.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.187886 restraints weight = 34180.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.191412 restraints weight = 23155.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.193525 restraints weight = 17793.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.194696 restraints weight = 15030.410| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.158 Angle : 0.619 5.352 14852 Z= 0.328 Chirality : 0.040 0.169 1784 Planarity : 0.004 0.045 1872 Dihedral : 5.564 19.752 1536 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.21), residues: 1412 helix: -1.59 (0.18), residues: 716 sheet: -3.37 (0.64), residues: 40 loop : -2.63 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.008 0.002 TYR A 10 PHE 0.032 0.002 PHE C 214 TRP 0.021 0.001 TRP A 206 HIS 0.012 0.003 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00316 (10880) covalent geometry : angle 0.61937 (14852) hydrogen bonds : bond 0.04755 ( 520) hydrogen bonds : angle 5.76677 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.3144 (ptt) cc_final: -0.3632 (ptt) REVERT: A 346 LEU cc_start: 0.8334 (mt) cc_final: 0.8024 (tt) REVERT: B 247 ILE cc_start: 0.8978 (pt) cc_final: 0.8484 (tp) REVERT: B 307 ARG cc_start: 0.6015 (mmm160) cc_final: 0.5745 (mmm160) REVERT: B 346 LEU cc_start: 0.8195 (mt) cc_final: 0.7976 (tt) REVERT: C 59 THR cc_start: 0.7065 (p) cc_final: 0.6678 (p) REVERT: C 164 GLN cc_start: 0.6542 (mp10) cc_final: 0.5916 (mp10) REVERT: C 217 GLU cc_start: 0.7958 (tp30) cc_final: 0.7715 (tp30) REVERT: C 346 LEU cc_start: 0.8286 (mt) cc_final: 0.8033 (tt) REVERT: D 155 GLN cc_start: 0.7175 (mt0) cc_final: 0.6823 (mt0) REVERT: D 164 GLN cc_start: 0.6500 (mp10) cc_final: 0.5892 (mp10) REVERT: D 197 MET cc_start: 0.8554 (tpp) cc_final: 0.8145 (tpp) REVERT: D 346 LEU cc_start: 0.8123 (mt) cc_final: 0.7910 (tt) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1798 time to fit residues: 101.3526 Evaluate side-chains 340 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 237 GLN D 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.220620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.181003 restraints weight = 60875.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.186562 restraints weight = 34533.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190068 restraints weight = 23408.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.192180 restraints weight = 18030.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193361 restraints weight = 15224.422| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.170 Angle : 0.625 5.398 14852 Z= 0.330 Chirality : 0.040 0.142 1784 Planarity : 0.004 0.043 1872 Dihedral : 5.390 20.722 1536 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.21), residues: 1412 helix: -1.52 (0.17), residues: 748 sheet: -3.49 (0.67), residues: 40 loop : -2.75 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.011 0.002 TYR C 178 PHE 0.027 0.002 PHE B 214 TRP 0.017 0.001 TRP A 206 HIS 0.007 0.003 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00332 (10880) covalent geometry : angle 0.62484 (14852) hydrogen bonds : bond 0.04638 ( 520) hydrogen bonds : angle 5.68142 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.7067 (p) cc_final: 0.6578 (p) REVERT: A 164 GLN cc_start: 0.6461 (mp10) cc_final: 0.5739 (mp10) REVERT: A 346 LEU cc_start: 0.8386 (mt) cc_final: 0.8001 (tt) REVERT: B 59 THR cc_start: 0.7165 (p) cc_final: 0.6665 (p) REVERT: B 247 ILE cc_start: 0.8812 (pt) cc_final: 0.8229 (tp) REVERT: B 307 ARG cc_start: 0.6035 (mmm160) cc_final: 0.5669 (mmm160) REVERT: B 346 LEU cc_start: 0.8192 (mt) cc_final: 0.7939 (tt) REVERT: C 59 THR cc_start: 0.7139 (p) cc_final: 0.6655 (p) REVERT: C 164 GLN cc_start: 0.6523 (mp10) cc_final: 0.5840 (mp10) REVERT: C 217 GLU cc_start: 0.7847 (tp30) cc_final: 0.7630 (tp30) REVERT: C 346 LEU cc_start: 0.8326 (mt) cc_final: 0.8008 (tt) REVERT: D 59 THR cc_start: 0.7199 (p) cc_final: 0.6675 (p) REVERT: D 118 LEU cc_start: 0.8053 (tt) cc_final: 0.7833 (tt) REVERT: D 155 GLN cc_start: 0.6969 (mt0) cc_final: 0.6493 (mt0) REVERT: D 164 GLN cc_start: 0.6382 (mp10) cc_final: 0.5667 (mp10) REVERT: D 189 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7944 (mtt90) REVERT: D 197 MET cc_start: 0.8534 (tpp) cc_final: 0.8127 (tpp) REVERT: D 206 TRP cc_start: 0.8005 (t60) cc_final: 0.7703 (t60) REVERT: D 346 LEU cc_start: 0.8182 (mt) cc_final: 0.7976 (tt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1742 time to fit residues: 97.8566 Evaluate side-chains 340 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 69 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 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 = 0.4591 r_free = 0.4591 target = 0.219458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.180862 restraints weight = 60628.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.186444 restraints weight = 33750.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.189928 restraints weight = 22620.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.191987 restraints weight = 17347.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193253 restraints weight = 14542.460| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10880 Z= 0.155 Angle : 0.596 5.330 14852 Z= 0.315 Chirality : 0.039 0.128 1784 Planarity : 0.005 0.053 1872 Dihedral : 5.230 19.626 1536 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.21), residues: 1412 helix: -1.28 (0.18), residues: 752 sheet: -3.54 (0.69), residues: 40 loop : -2.66 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.011 0.002 TYR C 178 PHE 0.051 0.002 PHE B 214 TRP 0.018 0.001 TRP A 206 HIS 0.005 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00311 (10880) covalent geometry : angle 0.59558 (14852) hydrogen bonds : bond 0.04323 ( 520) hydrogen bonds : angle 5.51728 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.7117 (p) cc_final: 0.6611 (p) REVERT: A 346 LEU cc_start: 0.8334 (mt) cc_final: 0.8060 (tt) REVERT: B 59 THR cc_start: 0.7188 (p) cc_final: 0.6634 (p) REVERT: B 247 ILE cc_start: 0.8825 (pt) cc_final: 0.8271 (tp) REVERT: B 272 MET cc_start: 0.6026 (ptm) cc_final: 0.5796 (ptm) REVERT: B 307 ARG cc_start: 0.6092 (mmm160) cc_final: 0.5711 (mmm160) REVERT: B 346 LEU cc_start: 0.8149 (mt) cc_final: 0.7897 (tt) REVERT: C 164 GLN cc_start: 0.6527 (mp10) cc_final: 0.5770 (mp10) REVERT: C 217 GLU cc_start: 0.7836 (tp30) cc_final: 0.7624 (tp30) REVERT: C 346 LEU cc_start: 0.8324 (mt) cc_final: 0.8002 (tt) REVERT: D 59 THR cc_start: 0.7080 (p) cc_final: 0.6455 (p) REVERT: D 155 GLN cc_start: 0.6944 (mt0) cc_final: 0.6486 (mt0) REVERT: D 197 MET cc_start: 0.8573 (tpp) cc_final: 0.8178 (tpp) REVERT: D 206 TRP cc_start: 0.7919 (t60) cc_final: 0.7653 (t60) REVERT: D 217 GLU cc_start: 0.7780 (tp30) cc_final: 0.7388 (tp30) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1769 time to fit residues: 98.8984 Evaluate side-chains 339 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 0.0060 chunk 118 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 overall best weight: 4.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4602 r_free = 0.4602 target = 0.220076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.180460 restraints weight = 61366.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.186170 restraints weight = 34586.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.189726 restraints weight = 23325.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.191841 restraints weight = 17947.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.193141 restraints weight = 15229.797| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.121 Angle : 0.571 5.340 14852 Z= 0.297 Chirality : 0.039 0.123 1784 Planarity : 0.004 0.046 1872 Dihedral : 5.000 20.133 1536 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.22), residues: 1412 helix: -0.73 (0.19), residues: 728 sheet: -3.54 (0.70), residues: 40 loop : -2.58 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.008 0.001 TYR A 10 PHE 0.045 0.002 PHE D 214 TRP 0.015 0.001 TRP B 168 HIS 0.004 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00256 (10880) covalent geometry : angle 0.57093 (14852) hydrogen bonds : bond 0.04023 ( 520) hydrogen bonds : angle 5.27562 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8312 (mt) cc_final: 0.8046 (tt) REVERT: B 33 MET cc_start: 0.5950 (mmm) cc_final: 0.5658 (mmm) REVERT: B 247 ILE cc_start: 0.8825 (pt) cc_final: 0.8261 (tp) REVERT: C 164 GLN cc_start: 0.6509 (mp10) cc_final: 0.5740 (mp10) REVERT: C 346 LEU cc_start: 0.8313 (mt) cc_final: 0.7998 (tt) REVERT: D 118 LEU cc_start: 0.7781 (tt) cc_final: 0.7494 (tt) REVERT: D 155 GLN cc_start: 0.6732 (mt0) cc_final: 0.6269 (mt0) REVERT: D 164 GLN cc_start: 0.6413 (mp10) cc_final: 0.5579 (mp10) REVERT: D 184 GLN cc_start: 0.7882 (mt0) cc_final: 0.7576 (mp10) REVERT: D 189 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.8034 (mtt180) REVERT: D 197 MET cc_start: 0.8604 (tpp) cc_final: 0.8223 (tpp) REVERT: D 217 GLU cc_start: 0.7651 (tp30) cc_final: 0.7277 (tp30) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1918 time to fit residues: 104.4392 Evaluate side-chains 336 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 136 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 64 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 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 = 0.4559 r_free = 0.4559 target = 0.216226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178412 restraints weight = 61424.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.183803 restraints weight = 34308.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.187187 restraints weight = 23184.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.188924 restraints weight = 17867.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.190305 restraints weight = 15384.149| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10880 Z= 0.179 Angle : 0.615 5.640 14852 Z= 0.328 Chirality : 0.040 0.133 1784 Planarity : 0.005 0.047 1872 Dihedral : 5.102 20.577 1536 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.22), residues: 1412 helix: -0.92 (0.18), residues: 736 sheet: -3.55 (0.73), residues: 40 loop : -2.42 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 71 TYR 0.014 0.002 TYR B 178 PHE 0.037 0.002 PHE C 214 TRP 0.012 0.002 TRP A 206 HIS 0.004 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00355 (10880) covalent geometry : angle 0.61468 (14852) hydrogen bonds : bond 0.04220 ( 520) hydrogen bonds : angle 5.34290 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8390 (mtt-85) cc_final: 0.8030 (mtt180) REVERT: A 217 GLU cc_start: 0.7779 (tp30) cc_final: 0.7577 (tp30) REVERT: A 346 LEU cc_start: 0.8392 (mt) cc_final: 0.8130 (tt) REVERT: B 59 THR cc_start: 0.7300 (p) cc_final: 0.6939 (p) REVERT: B 164 GLN cc_start: 0.6428 (mp10) cc_final: 0.5669 (mp10) REVERT: B 196 MET cc_start: 0.8633 (mpp) cc_final: 0.8429 (mpp) REVERT: B 220 ARG cc_start: 0.7837 (tpt-90) cc_final: 0.7519 (tpt-90) REVERT: B 247 ILE cc_start: 0.8788 (pt) cc_final: 0.8187 (tp) REVERT: C 346 LEU cc_start: 0.8341 (mt) cc_final: 0.8026 (tt) REVERT: D 59 THR cc_start: 0.7164 (p) cc_final: 0.6736 (p) REVERT: D 155 GLN cc_start: 0.6918 (mt0) cc_final: 0.6363 (mt0) REVERT: D 184 GLN cc_start: 0.8105 (mt0) cc_final: 0.7622 (mp10) REVERT: D 189 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8091 (mtt180) REVERT: D 217 GLU cc_start: 0.7785 (tp30) cc_final: 0.7447 (tp30) REVERT: D 248 VAL cc_start: 0.9077 (m) cc_final: 0.8876 (t) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1923 time to fit residues: 107.0085 Evaluate side-chains 346 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 78 optimal weight: 0.0670 chunk 118 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 overall best weight: 4.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.218317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.179529 restraints weight = 62155.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.185270 restraints weight = 34464.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.188866 restraints weight = 23124.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.190723 restraints weight = 17744.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.192021 restraints weight = 15265.936| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10880 Z= 0.120 Angle : 0.573 5.460 14852 Z= 0.300 Chirality : 0.039 0.121 1784 Planarity : 0.005 0.046 1872 Dihedral : 4.873 19.327 1536 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.18 % Allowed : 0.00 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.22), residues: 1412 helix: -0.62 (0.19), residues: 732 sheet: -3.09 (0.59), residues: 64 loop : -2.28 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.009 0.001 TYR A 10 PHE 0.037 0.002 PHE D 214 TRP 0.036 0.002 TRP A 206 HIS 0.003 0.002 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00254 (10880) covalent geometry : angle 0.57338 (14852) hydrogen bonds : bond 0.03901 ( 520) hydrogen bonds : angle 5.10677 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8374 (mt) cc_final: 0.8113 (tt) REVERT: B 33 MET cc_start: 0.5940 (mmm) cc_final: 0.5732 (mmm) REVERT: B 59 THR cc_start: 0.7170 (p) cc_final: 0.6778 (p) REVERT: B 247 ILE cc_start: 0.8720 (pt) cc_final: 0.8059 (tp) REVERT: C 346 LEU cc_start: 0.8333 (mt) cc_final: 0.8018 (tt) REVERT: D 59 THR cc_start: 0.7216 (p) cc_final: 0.6799 (p) REVERT: D 118 LEU cc_start: 0.7852 (tt) cc_final: 0.7420 (tt) REVERT: D 155 GLN cc_start: 0.6700 (mt0) cc_final: 0.6237 (mt0) REVERT: D 184 GLN cc_start: 0.7926 (mt0) cc_final: 0.7552 (mp10) REVERT: D 189 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7954 (mtt180) outliers start: 2 outliers final: 2 residues processed: 360 average time/residue: 0.1853 time to fit residues: 97.7044 Evaluate side-chains 331 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 92 optimal weight: 10.0000 overall best weight: 6.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4568 r_free = 0.4568 target = 0.217658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179279 restraints weight = 62684.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.184727 restraints weight = 35403.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.188242 restraints weight = 23962.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.190409 restraints weight = 18429.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191475 restraints weight = 15583.449| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10880 Z= 0.143 Angle : 0.578 5.401 14852 Z= 0.304 Chirality : 0.039 0.125 1784 Planarity : 0.005 0.045 1872 Dihedral : 4.824 19.666 1536 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.22), residues: 1412 helix: -0.60 (0.19), residues: 732 sheet: -3.12 (0.58), residues: 64 loop : -2.20 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 220 TYR 0.010 0.002 TYR D 178 PHE 0.028 0.002 PHE C 214 TRP 0.027 0.002 TRP A 206 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00297 (10880) covalent geometry : angle 0.57817 (14852) hydrogen bonds : bond 0.03864 ( 520) hydrogen bonds : angle 5.09673 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.10 seconds wall clock time: 58 minutes 31.75 seconds (3511.75 seconds total)