Starting phenix.real_space_refine on Thu Mar 5 09:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qd0_4515/03_2026/6qd0_4515.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd0_4515/03_2026/6qd0_4515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qd0_4515/03_2026/6qd0_4515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd0_4515/03_2026/6qd0_4515.map" model { file = "/net/cci-nas-00/data/ceres_data/6qd0_4515/03_2026/6qd0_4515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd0_4515/03_2026/6qd0_4515.cif" } resolution = 4.5 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: 5 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.72, per 1000 atoms: 0.17 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 102.7, 93.6, 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: 1.87 Conformation dependent library (CDL) restraints added in 633.5 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: 64 helices and 12 sheets defined 65.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.515A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.546A pdb=" N ALA A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.807A pdb=" N ILE A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 61 removed outlier: 3.666A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.711A pdb=" N ILE A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.688A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 103 through 104 No H-bonds generated for 'chain 'A' and resid 103 through 104' Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.164A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 152 removed outlier: 4.003A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.098A 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 162 through 174 removed outlier: 3.651A pdb=" N TRP A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 225 removed outlier: 3.560A pdb=" N ARG A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (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: 3.918A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.514A pdb=" N LEU B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.545A pdb=" N ALA B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.807A pdb=" N ILE B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 61 removed outlier: 3.666A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 92 removed outlier: 4.712A pdb=" N ILE B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 3.688A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 103 through 104 No H-bonds generated for 'chain 'B' and resid 103 through 104' Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.163A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 152 removed outlier: 4.002A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 4.098A 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 162 through 174 removed outlier: 3.653A pdb=" N TRP B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 225 removed outlier: 3.559A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N MET B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 249 " --> pdb=" O VAL B 245 " (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: 3.918A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.514A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.545A pdb=" N ALA C 24 " --> pdb=" O PRO C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.807A pdb=" N ILE C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 61 removed outlier: 3.665A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 4.711A pdb=" N ILE C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.688A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 103 through 104 No H-bonds generated for 'chain 'C' and resid 103 through 104' Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.163A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 152 removed outlier: 4.003A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.098A 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 162 through 174 removed outlier: 3.652A pdb=" N TRP C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 225 removed outlier: 3.560A pdb=" N ARG C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG C 249 " --> pdb=" O VAL C 245 " (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: 3.918A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 removed outlier: 3.515A pdb=" N LEU D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.546A pdb=" N ALA D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.808A pdb=" N ILE D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 61 removed outlier: 3.666A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 removed outlier: 4.711A pdb=" N ILE D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.687A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 104 No H-bonds generated for 'chain 'D' and resid 103 through 104' Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.163A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 152 removed outlier: 4.003A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 4.098A 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 162 through 174 removed outlier: 3.653A pdb=" N TRP D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 225 removed outlier: 3.559A pdb=" N ARG D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG D 249 " --> pdb=" O VAL D 245 " (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: 3.919A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 320 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 275 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 320 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 275 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.588A pdb=" N VAL A 311 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 310 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 320 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 275 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 320 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 275 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 263 removed outlier: 6.588A pdb=" N VAL B 311 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR B 310 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 320 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 275 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 320 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 275 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 261 through 263 removed outlier: 6.588A pdb=" N VAL C 311 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 310 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 320 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL D 275 " --> pdb=" O LEU D 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 320 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL D 275 " --> pdb=" O LEU D 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 261 through 263 removed outlier: 6.587A pdb=" N VAL D 311 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR D 310 " --> pdb=" O ALA D 283 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11088 1.03 - 1.22: 12 1.22 - 1.42: 4343 1.42 - 1.61: 6461 1.61 - 1.80: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" CB LEU B 106 " pdb=" HB3 LEU B 106 " ideal model delta sigma weight residual 0.970 1.012 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" CB LEU A 106 " pdb=" HB3 LEU A 106 " ideal model delta sigma weight residual 0.970 1.012 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" CB LEU D 106 " pdb=" HB3 LEU D 106 " ideal model delta sigma weight residual 0.970 1.012 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" CB LEU C 106 " pdb=" HB3 LEU C 106 " ideal model delta sigma weight residual 0.970 1.011 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" CZ ARG A 220 " pdb=" NH2 ARG A 220 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.81e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 37292 1.81 - 3.61: 2362 3.61 - 5.42: 268 5.42 - 7.22: 13 7.22 - 9.03: 5 Bond angle restraints: 39940 Sorted by residual: angle pdb=" CG HIS B 323 " pdb=" CB HIS B 323 " pdb=" HB3 HIS B 323 " ideal model delta sigma weight residual 108.00 98.97 9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" N ALA B 294 " pdb=" CA ALA B 294 " pdb=" C ALA B 294 " ideal model delta sigma weight residual 108.45 112.19 -3.74 1.26e+00 6.30e-01 8.80e+00 angle pdb=" N ALA A 294 " pdb=" CA ALA A 294 " pdb=" C ALA A 294 " ideal model delta sigma weight residual 108.45 112.18 -3.73 1.26e+00 6.30e-01 8.74e+00 angle pdb=" N ALA C 294 " pdb=" CA ALA C 294 " pdb=" C ALA C 294 " ideal model delta sigma weight residual 108.45 112.16 -3.71 1.26e+00 6.30e-01 8.66e+00 angle pdb=" N ALA D 294 " pdb=" CA ALA D 294 " pdb=" C ALA D 294 " ideal model delta sigma weight residual 108.45 112.14 -3.69 1.26e+00 6.30e-01 8.58e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 9419 15.47 - 30.93: 575 30.93 - 46.40: 186 46.40 - 61.87: 100 61.87 - 77.34: 8 Dihedral angle restraints: 10288 sinusoidal: 5604 harmonic: 4684 Sorted by residual: dihedral pdb=" CA ASN D 226 " pdb=" C ASN D 226 " pdb=" N TRP D 227 " pdb=" CA TRP D 227 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASN A 226 " pdb=" C ASN A 226 " pdb=" N TRP A 227 " pdb=" CA TRP A 227 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN B 226 " pdb=" C ASN B 226 " pdb=" N TRP B 227 " pdb=" CA TRP B 227 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 10285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 879 0.029 - 0.057: 531 0.057 - 0.086: 225 0.086 - 0.115: 105 0.115 - 0.143: 44 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA VAL A 288 " pdb=" N VAL A 288 " pdb=" C VAL A 288 " pdb=" CB VAL A 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA VAL D 288 " pdb=" N VAL D 288 " pdb=" C VAL D 288 " pdb=" CB VAL D 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL B 288 " pdb=" N VAL B 288 " pdb=" C VAL B 288 " pdb=" CB VAL B 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" N ALA A 325 " -0.040 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.010 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C LEU A 210 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 210 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 211 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LEU D 210 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU D 210 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 211 " -0.013 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.35: 8011 2.35 - 3.05: 64371 3.05 - 3.75: 74419 3.75 - 4.44: 116971 4.44 - 5.14: 176277 Nonbonded interactions: 440049 Sorted by model distance: nonbonded pdb=" H GLY C 259 " pdb=" O ALA C 313 " model vdw 1.654 2.450 nonbonded pdb=" H GLY D 259 " pdb=" O ALA D 313 " model vdw 1.655 2.450 nonbonded pdb=" H GLY A 259 " pdb=" O ALA A 313 " model vdw 1.655 2.450 nonbonded pdb=" H GLY B 259 " pdb=" O ALA B 313 " model vdw 1.655 2.450 nonbonded pdb=" O PRO A 234 " pdb="HE22 GLN A 237 " model vdw 1.661 2.450 ... (remaining 440044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 355) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.030 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: 0.180 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.340 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 0.047 10880 Z= 0.432 Angle : 1.026 8.406 14852 Z= 0.568 Chirality : 0.048 0.143 1784 Planarity : 0.007 0.046 1872 Dihedral : 9.680 77.336 3844 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -4.94 (0.19), residues: 1412 helix: -4.10 (0.11), residues: 660 sheet: -4.42 (0.41), residues: 40 loop : -2.28 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 254 TYR 0.021 0.004 TYR D 178 PHE 0.026 0.003 PHE B 203 TRP 0.014 0.003 TRP C 206 HIS 0.005 0.003 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00893 (10880) covalent geometry : angle 1.02561 (14852) hydrogen bonds : bond 0.32046 ( 516) hydrogen bonds : angle 12.51889 ( 1452) *********************** 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 408 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.501 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: A 95 PRO cc_start: 0.8100 (Cg_exo) cc_final: 0.7749 (Cg_endo) REVERT: A 223 PHE cc_start: 0.6441 (t80) cc_final: 0.5909 (t80) REVERT: A 243 VAL cc_start: 0.9287 (t) cc_final: 0.9048 (m) REVERT: B 95 PRO cc_start: 0.8091 (Cg_exo) cc_final: 0.7805 (Cg_endo) REVERT: B 223 PHE cc_start: 0.6601 (t80) cc_final: 0.6126 (t80) REVERT: B 243 VAL cc_start: 0.9289 (t) cc_final: 0.9060 (m) REVERT: C 95 PRO cc_start: 0.8200 (Cg_exo) cc_final: 0.7962 (Cg_endo) REVERT: C 223 PHE cc_start: 0.6630 (t80) cc_final: 0.6132 (t80) REVERT: C 243 VAL cc_start: 0.9299 (t) cc_final: 0.9063 (m) REVERT: C 328 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8819 (tp-100) REVERT: D 33 MET cc_start: 0.5940 (mmm) cc_final: 0.5605 (mmm) REVERT: D 173 LEU cc_start: 0.8488 (tp) cc_final: 0.8269 (tp) REVERT: D 243 VAL cc_start: 0.9317 (t) cc_final: 0.9076 (m) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2635 time to fit residues: 147.0346 Evaluate side-chains 262 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN C 216 GLN D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.176386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142439 restraints weight = 68080.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.148600 restraints weight = 34005.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.152609 restraints weight = 20521.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.155324 restraints weight = 14361.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156955 restraints weight = 11162.376| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10880 Z= 0.181 Angle : 0.707 6.965 14852 Z= 0.385 Chirality : 0.042 0.147 1784 Planarity : 0.007 0.047 1872 Dihedral : 6.631 23.689 1536 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -3.44 (0.21), residues: 1412 helix: -2.12 (0.17), residues: 632 sheet: -3.81 (0.55), residues: 40 loop : -2.33 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 220 TYR 0.014 0.002 TYR A 100 PHE 0.015 0.002 PHE A 223 TRP 0.015 0.001 TRP B 167 HIS 0.004 0.002 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00349 (10880) covalent geometry : angle 0.70730 (14852) hydrogen bonds : bond 0.07072 ( 516) hydrogen bonds : angle 7.41176 ( 1452) *********************** 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 320 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.571 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: A 105 LEU cc_start: 0.8750 (mm) cc_final: 0.8477 (mm) REVERT: A 275 VAL cc_start: 0.8404 (t) cc_final: 0.8036 (m) REVERT: A 328 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8504 (tp-100) REVERT: B 105 LEU cc_start: 0.8868 (mm) cc_final: 0.8662 (mm) REVERT: B 243 VAL cc_start: 0.9311 (t) cc_final: 0.9084 (m) REVERT: B 275 VAL cc_start: 0.8330 (t) cc_final: 0.8018 (m) REVERT: C 52 TYR cc_start: 0.7501 (m-10) cc_final: 0.6924 (m-10) REVERT: C 74 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7728 (mtpp) REVERT: C 105 LEU cc_start: 0.8737 (mm) cc_final: 0.8445 (mm) REVERT: C 117 VAL cc_start: 0.7809 (t) cc_final: 0.7582 (t) REVERT: C 243 VAL cc_start: 0.9253 (t) cc_final: 0.8989 (m) REVERT: C 275 VAL cc_start: 0.8307 (t) cc_final: 0.7981 (m) REVERT: D 33 MET cc_start: 0.5875 (mmm) cc_final: 0.5365 (mmp) REVERT: D 243 VAL cc_start: 0.9255 (t) cc_final: 0.8975 (m) REVERT: D 275 VAL cc_start: 0.8478 (t) cc_final: 0.8145 (m) REVERT: D 328 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8406 (tp-100) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2238 time to fit residues: 102.8156 Evaluate side-chains 255 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 8.9990 chunk 136 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 27 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.173563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.140178 restraints weight = 68743.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.146053 restraints weight = 34377.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.149957 restraints weight = 20879.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152508 restraints weight = 14661.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.154118 restraints weight = 11526.065| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4653 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= 0.153 Angle : 0.628 5.748 14852 Z= 0.342 Chirality : 0.040 0.133 1784 Planarity : 0.006 0.042 1872 Dihedral : 5.971 21.014 1536 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -3.11 (0.21), residues: 1412 helix: -1.57 (0.18), residues: 680 sheet: -3.28 (0.67), residues: 40 loop : -2.49 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.014 0.002 TYR A 178 PHE 0.013 0.001 PHE A 136 TRP 0.015 0.001 TRP A 227 HIS 0.001 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00306 (10880) covalent geometry : angle 0.62793 (14852) hydrogen bonds : bond 0.05954 ( 516) hydrogen bonds : angle 6.78521 ( 1452) *********************** 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 341 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.588 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: A 105 LEU cc_start: 0.8784 (mm) cc_final: 0.8512 (mm) REVERT: A 106 LEU cc_start: 0.9487 (mt) cc_final: 0.9210 (pp) REVERT: A 125 GLU cc_start: 0.8698 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 223 PHE cc_start: 0.6635 (t80) cc_final: 0.6251 (t80) REVERT: A 275 VAL cc_start: 0.8543 (t) cc_final: 0.8210 (m) REVERT: B 52 TYR cc_start: 0.7688 (m-10) cc_final: 0.7147 (m-10) REVERT: B 105 LEU cc_start: 0.8861 (mm) cc_final: 0.8654 (mm) REVERT: B 106 LEU cc_start: 0.9448 (mt) cc_final: 0.9205 (pp) REVERT: B 125 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7947 (mm-30) REVERT: B 140 LEU cc_start: 0.8325 (tt) cc_final: 0.7984 (tp) REVERT: B 243 VAL cc_start: 0.9290 (t) cc_final: 0.9083 (m) REVERT: B 275 VAL cc_start: 0.8383 (t) cc_final: 0.8001 (m) REVERT: C 105 LEU cc_start: 0.8775 (mm) cc_final: 0.8511 (mm) REVERT: C 125 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 243 VAL cc_start: 0.9227 (t) cc_final: 0.8948 (m) REVERT: C 275 VAL cc_start: 0.8496 (t) cc_final: 0.8138 (m) REVERT: D 33 MET cc_start: 0.5873 (mmm) cc_final: 0.5387 (mmp) REVERT: D 52 TYR cc_start: 0.7847 (m-10) cc_final: 0.7326 (m-10) REVERT: D 106 LEU cc_start: 0.9418 (mt) cc_final: 0.9141 (pp) REVERT: D 140 LEU cc_start: 0.8609 (tt) cc_final: 0.8332 (tp) REVERT: D 243 VAL cc_start: 0.9246 (t) cc_final: 0.8964 (m) REVERT: D 275 VAL cc_start: 0.8458 (t) cc_final: 0.8107 (m) REVERT: D 347 GLU cc_start: 0.8450 (tt0) cc_final: 0.8143 (tp30) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2054 time to fit residues: 103.0724 Evaluate side-chains 239 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 20.0000 chunk 109 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 25 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.168089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.133724 restraints weight = 71761.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.139240 restraints weight = 36196.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.142868 restraints weight = 22305.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.145139 restraints weight = 15998.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.146749 restraints weight = 12846.581| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10880 Z= 0.237 Angle : 0.680 5.414 14852 Z= 0.377 Chirality : 0.041 0.149 1784 Planarity : 0.006 0.043 1872 Dihedral : 5.871 21.354 1536 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 0.18 % Allowed : 1.37 % 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: -3.13 (0.21), residues: 1412 helix: -1.57 (0.18), residues: 712 sheet: -3.63 (0.62), residues: 40 loop : -2.52 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 220 TYR 0.016 0.002 TYR A 215 PHE 0.018 0.002 PHE C 341 TRP 0.019 0.002 TRP A 227 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00455 (10880) covalent geometry : angle 0.68048 (14852) hydrogen bonds : bond 0.05578 ( 516) hydrogen bonds : angle 6.52479 ( 1452) *********************** 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 296 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 0.524 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: A 33 MET cc_start: 0.6002 (mmm) cc_final: 0.5477 (mmm) REVERT: A 105 LEU cc_start: 0.8840 (mm) cc_final: 0.8575 (mm) REVERT: A 170 VAL cc_start: 0.8322 (t) cc_final: 0.8068 (p) REVERT: A 275 VAL cc_start: 0.8639 (t) cc_final: 0.8272 (m) REVERT: B 33 MET cc_start: 0.6108 (mmm) cc_final: 0.5669 (mmm) REVERT: B 105 LEU cc_start: 0.8877 (mm) cc_final: 0.8659 (mm) REVERT: B 170 VAL cc_start: 0.8377 (t) cc_final: 0.8147 (p) REVERT: B 173 LEU cc_start: 0.8487 (tt) cc_final: 0.8082 (tp) REVERT: B 275 VAL cc_start: 0.8412 (t) cc_final: 0.8064 (m) REVERT: C 170 VAL cc_start: 0.8377 (t) cc_final: 0.8105 (p) REVERT: C 243 VAL cc_start: 0.9340 (t) cc_final: 0.9131 (m) REVERT: C 275 VAL cc_start: 0.8700 (t) cc_final: 0.8362 (m) REVERT: C 327 PHE cc_start: 0.7054 (t80) cc_final: 0.6586 (t80) REVERT: C 328 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8559 (tp-100) REVERT: D 33 MET cc_start: 0.5609 (mmm) cc_final: 0.5155 (mmm) REVERT: D 52 TYR cc_start: 0.7833 (m-10) cc_final: 0.7285 (m-10) REVERT: D 105 LEU cc_start: 0.8880 (mm) cc_final: 0.8676 (mm) REVERT: D 170 VAL cc_start: 0.8428 (t) cc_final: 0.8176 (p) REVERT: D 173 LEU cc_start: 0.8668 (tt) cc_final: 0.8328 (tp) REVERT: D 243 VAL cc_start: 0.9340 (t) cc_final: 0.9114 (m) REVERT: D 275 VAL cc_start: 0.8473 (t) cc_final: 0.8123 (m) REVERT: D 347 GLU cc_start: 0.8469 (tt0) cc_final: 0.8130 (tp30) outliers start: 2 outliers final: 2 residues processed: 296 average time/residue: 0.2083 time to fit residues: 89.6888 Evaluate side-chains 229 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 8.9990 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 40.0000 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4361 r_free = 0.4361 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136088 restraints weight = 69647.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141722 restraints weight = 34561.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.145451 restraints weight = 21138.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.147853 restraints weight = 15092.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.149370 restraints weight = 12095.957| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10880 Z= 0.162 Angle : 0.608 5.362 14852 Z= 0.330 Chirality : 0.040 0.139 1784 Planarity : 0.005 0.037 1872 Dihedral : 5.585 20.046 1536 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -2.89 (0.22), residues: 1412 helix: -1.26 (0.18), residues: 736 sheet: -3.46 (0.65), residues: 40 loop : -2.60 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.020 0.002 TYR D 178 PHE 0.014 0.002 PHE C 186 TRP 0.017 0.002 TRP D 227 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00322 (10880) covalent geometry : angle 0.60786 (14852) hydrogen bonds : bond 0.04910 ( 516) hydrogen bonds : angle 6.21420 ( 1452) *********************** 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 298 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.442 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: A 105 LEU cc_start: 0.8776 (mm) cc_final: 0.8504 (mm) REVERT: A 125 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 170 VAL cc_start: 0.8416 (t) cc_final: 0.8142 (p) REVERT: A 275 VAL cc_start: 0.8617 (t) cc_final: 0.8261 (m) REVERT: B 33 MET cc_start: 0.6149 (mmm) cc_final: 0.5684 (mmm) REVERT: B 105 LEU cc_start: 0.8822 (mm) cc_final: 0.8608 (mm) REVERT: B 125 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 275 VAL cc_start: 0.8443 (t) cc_final: 0.8112 (m) REVERT: B 327 PHE cc_start: 0.7160 (t80) cc_final: 0.6837 (t80) REVERT: C 105 LEU cc_start: 0.8763 (mm) cc_final: 0.8448 (mm) REVERT: C 125 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7942 (mm-30) REVERT: C 129 LEU cc_start: 0.9216 (mt) cc_final: 0.8964 (tt) REVERT: C 217 GLU cc_start: 0.8764 (tp30) cc_final: 0.8359 (tp30) REVERT: C 275 VAL cc_start: 0.8761 (t) cc_final: 0.8406 (m) REVERT: D 33 MET cc_start: 0.5620 (mmm) cc_final: 0.5098 (mmm) REVERT: D 105 LEU cc_start: 0.8764 (mm) cc_final: 0.8530 (mm) REVERT: D 243 VAL cc_start: 0.9361 (t) cc_final: 0.9157 (m) REVERT: D 275 VAL cc_start: 0.8492 (t) cc_final: 0.8129 (m) REVERT: D 347 GLU cc_start: 0.8472 (tt0) cc_final: 0.8122 (tp30) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1928 time to fit residues: 84.1250 Evaluate side-chains 233 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 20.0000 chunk 55 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 31 optimal weight: 50.0000 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.172069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135243 restraints weight = 76606.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.140921 restraints weight = 39649.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.144679 restraints weight = 25126.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.147107 restraints weight = 18339.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.148434 restraints weight = 14868.887| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10880 Z= 0.144 Angle : 0.582 5.099 14852 Z= 0.314 Chirality : 0.040 0.137 1784 Planarity : 0.005 0.039 1872 Dihedral : 5.304 18.874 1536 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -2.70 (0.22), residues: 1412 helix: -1.00 (0.18), residues: 748 sheet: -3.30 (0.67), residues: 40 loop : -2.69 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.020 0.002 TYR C 178 PHE 0.012 0.001 PHE A 203 TRP 0.018 0.002 TRP B 227 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00288 (10880) covalent geometry : angle 0.58184 (14852) hydrogen bonds : bond 0.04453 ( 516) hydrogen bonds : angle 5.93085 ( 1452) *********************** 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 286 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.519 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: A 105 LEU cc_start: 0.8717 (mm) cc_final: 0.8472 (mm) REVERT: A 275 VAL cc_start: 0.8722 (t) cc_final: 0.8395 (m) REVERT: A 327 PHE cc_start: 0.7213 (t80) cc_final: 0.6849 (t80) REVERT: B 105 LEU cc_start: 0.8793 (mm) cc_final: 0.8581 (mm) REVERT: B 125 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 275 VAL cc_start: 0.8515 (t) cc_final: 0.8203 (m) REVERT: C 105 LEU cc_start: 0.8718 (mm) cc_final: 0.8400 (mm) REVERT: C 129 LEU cc_start: 0.9224 (mt) cc_final: 0.9013 (tt) REVERT: C 275 VAL cc_start: 0.8672 (t) cc_final: 0.8330 (m) REVERT: D 33 MET cc_start: 0.5662 (mmm) cc_final: 0.5114 (mmm) REVERT: D 74 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8380 (mmmt) REVERT: D 105 LEU cc_start: 0.8770 (mm) cc_final: 0.8553 (mm) REVERT: D 275 VAL cc_start: 0.8594 (t) cc_final: 0.8245 (m) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2141 time to fit residues: 87.9698 Evaluate side-chains 232 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 30.0000 chunk 37 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.167800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133664 restraints weight = 75221.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139005 restraints weight = 37705.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.142691 restraints weight = 23129.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.145068 restraints weight = 16336.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.146634 restraints weight = 12918.356| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10880 Z= 0.153 Angle : 0.573 5.158 14852 Z= 0.309 Chirality : 0.039 0.141 1784 Planarity : 0.005 0.039 1872 Dihedral : 5.124 17.697 1536 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % 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: -2.49 (0.22), residues: 1412 helix: -0.86 (0.18), residues: 768 sheet: -3.38 (0.64), residues: 40 loop : -2.55 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 220 TYR 0.010 0.002 TYR A 215 PHE 0.017 0.002 PHE C 341 TRP 0.018 0.002 TRP B 227 HIS 0.003 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00305 (10880) covalent geometry : angle 0.57253 (14852) hydrogen bonds : bond 0.04229 ( 516) hydrogen bonds : angle 5.72684 ( 1452) *********************** 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 283 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.474 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: A 105 LEU cc_start: 0.8703 (mm) cc_final: 0.8424 (mm) REVERT: A 275 VAL cc_start: 0.8815 (t) cc_final: 0.8470 (m) REVERT: B 105 LEU cc_start: 0.8727 (mm) cc_final: 0.8477 (mm) REVERT: B 275 VAL cc_start: 0.8671 (t) cc_final: 0.8323 (m) REVERT: B 327 PHE cc_start: 0.7284 (t80) cc_final: 0.6953 (t80) REVERT: C 105 LEU cc_start: 0.8652 (mm) cc_final: 0.8329 (mm) REVERT: C 129 LEU cc_start: 0.9217 (mt) cc_final: 0.9011 (tt) REVERT: C 275 VAL cc_start: 0.8764 (t) cc_final: 0.8407 (m) REVERT: D 33 MET cc_start: 0.5800 (mmm) cc_final: 0.5262 (mmm) REVERT: D 105 LEU cc_start: 0.8711 (mm) cc_final: 0.8458 (mm) REVERT: D 243 VAL cc_start: 0.9353 (m) cc_final: 0.9142 (p) REVERT: D 275 VAL cc_start: 0.8677 (t) cc_final: 0.8317 (m) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2076 time to fit residues: 84.6798 Evaluate side-chains 241 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 9.9990 chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4342 r_free = 0.4342 target = 0.166216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130512 restraints weight = 78246.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.135885 restraints weight = 40554.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.139340 restraints weight = 25733.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.141549 restraints weight = 18964.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.142984 restraints weight = 15478.097| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.004 0.031 10880 Z= 0.190 Angle : 0.626 5.187 14852 Z= 0.343 Chirality : 0.041 0.152 1784 Planarity : 0.006 0.048 1872 Dihedral : 5.256 16.898 1536 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.19 (0.22), residues: 1412 helix: -0.73 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -2.30 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.018 0.002 TYR D 215 PHE 0.014 0.002 PHE C 223 TRP 0.022 0.002 TRP D 227 HIS 0.007 0.003 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00366 (10880) covalent geometry : angle 0.62613 (14852) hydrogen bonds : bond 0.04318 ( 516) hydrogen bonds : angle 5.76815 ( 1452) *********************** 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 276 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.413 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: A 105 LEU cc_start: 0.8682 (mm) cc_final: 0.8389 (mm) REVERT: A 275 VAL cc_start: 0.8940 (t) cc_final: 0.8575 (m) REVERT: B 105 LEU cc_start: 0.8725 (mm) cc_final: 0.8421 (mm) REVERT: B 197 MET cc_start: 0.8018 (tpp) cc_final: 0.7813 (tpp) REVERT: B 275 VAL cc_start: 0.8731 (t) cc_final: 0.8379 (m) REVERT: C 105 LEU cc_start: 0.8697 (mm) cc_final: 0.8385 (mm) REVERT: C 197 MET cc_start: 0.8061 (tpp) cc_final: 0.7800 (tpp) REVERT: C 275 VAL cc_start: 0.8860 (t) cc_final: 0.8503 (m) REVERT: D 33 MET cc_start: 0.5903 (mmm) cc_final: 0.5301 (mmm) REVERT: D 105 LEU cc_start: 0.8682 (mm) cc_final: 0.8372 (mm) REVERT: D 275 VAL cc_start: 0.8697 (t) cc_final: 0.8332 (m) REVERT: D 326 ASP cc_start: 0.9006 (m-30) cc_final: 0.8787 (m-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2051 time to fit residues: 81.8006 Evaluate side-chains 244 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 20.0000 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4352 r_free = 0.4352 target = 0.167563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131765 restraints weight = 73907.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.137304 restraints weight = 37228.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.140866 restraints weight = 23128.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143132 restraints weight = 16785.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.144642 restraints weight = 13630.665| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10880 Z= 0.160 Angle : 0.589 5.159 14852 Z= 0.317 Chirality : 0.040 0.137 1784 Planarity : 0.006 0.053 1872 Dihedral : 5.144 16.355 1536 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % 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: -2.16 (0.22), residues: 1412 helix: -0.56 (0.18), residues: 744 sheet: -3.37 (0.59), residues: 40 loop : -2.39 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 220 TYR 0.014 0.002 TYR C 148 PHE 0.019 0.001 PHE A 341 TRP 0.019 0.002 TRP C 227 HIS 0.009 0.004 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00315 (10880) covalent geometry : angle 0.58933 (14852) hydrogen bonds : bond 0.04101 ( 516) hydrogen bonds : angle 5.60767 ( 1452) *********************** 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 273 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.331 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 105 LEU cc_start: 0.8648 (mm) cc_final: 0.8351 (mm) REVERT: A 275 VAL cc_start: 0.8862 (t) cc_final: 0.8483 (m) REVERT: B 105 LEU cc_start: 0.8690 (mm) cc_final: 0.8367 (mm) REVERT: B 275 VAL cc_start: 0.8809 (t) cc_final: 0.8443 (m) REVERT: C 105 LEU cc_start: 0.8654 (mm) cc_final: 0.8338 (mm) REVERT: C 275 VAL cc_start: 0.8839 (t) cc_final: 0.8455 (m) REVERT: D 33 MET cc_start: 0.5885 (mmm) cc_final: 0.5466 (mmm) REVERT: D 105 LEU cc_start: 0.8643 (mm) cc_final: 0.8345 (mm) REVERT: D 275 VAL cc_start: 0.8746 (t) cc_final: 0.8369 (m) REVERT: D 326 ASP cc_start: 0.9037 (m-30) cc_final: 0.8771 (m-30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2051 time to fit residues: 80.9435 Evaluate side-chains 243 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 3.9990 chunk 127 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 100 optimal weight: 30.0000 chunk 41 optimal weight: 0.0060 chunk 78 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- 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 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 = 0.4373 r_free = 0.4373 target = 0.168213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135225 restraints weight = 72161.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.140119 restraints weight = 37552.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143436 restraints weight = 24176.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.145701 restraints weight = 17958.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.147189 restraints weight = 14796.662| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10880 Z= 0.117 Angle : 0.563 5.698 14852 Z= 0.298 Chirality : 0.039 0.117 1784 Planarity : 0.005 0.052 1872 Dihedral : 4.897 16.178 1536 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % 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: -1.89 (0.22), residues: 1412 helix: -0.20 (0.18), residues: 732 sheet: -3.00 (0.63), residues: 40 loop : -2.44 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 220 TYR 0.008 0.001 TYR A 10 PHE 0.016 0.001 PHE B 214 TRP 0.020 0.002 TRP A 227 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00247 (10880) covalent geometry : angle 0.56347 (14852) hydrogen bonds : bond 0.03732 ( 516) hydrogen bonds : angle 5.33415 ( 1452) ********************** 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 282 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.444 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 99 LEU cc_start: 0.9268 (mt) cc_final: 0.9022 (mm) REVERT: A 105 LEU cc_start: 0.8625 (mm) cc_final: 0.8296 (mm) REVERT: A 112 SER cc_start: 0.7191 (t) cc_final: 0.6985 (t) REVERT: A 275 VAL cc_start: 0.8968 (t) cc_final: 0.8617 (m) REVERT: B 38 ARG cc_start: 0.8693 (tpt170) cc_final: 0.8462 (tpt170) REVERT: B 105 LEU cc_start: 0.8644 (mm) cc_final: 0.8333 (mm) REVERT: B 275 VAL cc_start: 0.8801 (t) cc_final: 0.8448 (m) REVERT: B 327 PHE cc_start: 0.7150 (t80) cc_final: 0.6908 (t80) REVERT: C 105 LEU cc_start: 0.8635 (mm) cc_final: 0.8296 (mm) REVERT: C 125 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8083 (mm-30) REVERT: C 129 LEU cc_start: 0.9225 (mt) cc_final: 0.8981 (tt) REVERT: C 197 MET cc_start: 0.8019 (tpp) cc_final: 0.7799 (tpp) REVERT: C 275 VAL cc_start: 0.8969 (t) cc_final: 0.8579 (m) REVERT: D 33 MET cc_start: 0.5882 (mmm) cc_final: 0.5447 (mmm) REVERT: D 74 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8450 (mmmt) REVERT: D 105 LEU cc_start: 0.8631 (mm) cc_final: 0.8311 (mm) REVERT: D 275 VAL cc_start: 0.8842 (t) cc_final: 0.8439 (m) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2098 time to fit residues: 85.5420 Evaluate side-chains 250 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 2.9990 chunk 102 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 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 = 0.4351 r_free = 0.4351 target = 0.165547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131769 restraints weight = 72459.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.137032 restraints weight = 36259.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.140571 restraints weight = 22624.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.142894 restraints weight = 16541.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.144278 restraints weight = 13438.651| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10880 Z= 0.127 Angle : 0.558 6.082 14852 Z= 0.296 Chirality : 0.039 0.126 1784 Planarity : 0.005 0.053 1872 Dihedral : 4.814 16.091 1536 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % 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: -1.62 (0.22), residues: 1412 helix: -0.04 (0.19), residues: 748 sheet: -2.93 (0.64), residues: 40 loop : -2.25 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 220 TYR 0.010 0.002 TYR C 215 PHE 0.020 0.001 PHE D 341 TRP 0.023 0.002 TRP D 227 HIS 0.003 0.002 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00262 (10880) covalent geometry : angle 0.55842 (14852) hydrogen bonds : bond 0.03681 ( 516) hydrogen bonds : angle 5.24124 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.95 seconds wall clock time: 57 minutes 12.28 seconds (3432.28 seconds total)