Starting phenix.real_space_refine on Fri Mar 6 14:30:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o1q_12696/03_2026/7o1q_12696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o1q_12696/03_2026/7o1q_12696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o1q_12696/03_2026/7o1q_12696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o1q_12696/03_2026/7o1q_12696.map" model { file = "/net/cci-nas-00/data/ceres_data/7o1q_12696/03_2026/7o1q_12696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o1q_12696/03_2026/7o1q_12696.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 10402 2.51 5 N 2842 2.21 5 O 3220 1.98 5 H 15921 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s 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: 32434 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4636 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "B" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "C" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "D" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "E" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "F" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4633 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Time building chain proxies: 5.11, per 1000 atoms: 0.16 Number of scatterers: 32434 At special positions: 0 Unit cell: (112.27, 112.27, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 3220 8.00 N 2842 7.00 C 10402 6.00 H 15921 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 902.0 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 29 sheets defined 3.8% alpha, 58.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.010A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29 removed outlier: 6.577A pdb=" N THR A 233 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE A 98 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU A 70 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS A 75 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU A 70 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS A 75 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS A 75 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP A 260 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY A 77 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 258 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA A 79 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 256 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 83 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP A 255 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP A 272 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN A 257 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR A 270 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS A 259 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR A 268 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 127 removed outlier: 7.798A pdb=" N PHE A 109 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 149 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 143 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 136 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE G 124 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 138 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE G 109 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL G 149 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY G 143 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE G 136 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE F 124 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY G 138 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE F 109 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL F 149 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 143 " --> pdb=" O TYR F 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE F 136 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 124 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY F 138 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE E 109 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL E 149 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 143 " --> pdb=" O TYR E 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 136 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE D 124 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY E 138 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 109 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 149 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 143 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 136 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE C 124 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 138 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 109 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL C 149 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 143 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 136 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 124 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 138 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE B 109 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 149 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 143 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 136 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 124 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 138 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 29 removed outlier: 6.577A pdb=" N THR B 233 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 98 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS B 75 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TRP B 260 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY B 77 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 258 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA B 79 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR B 256 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 254 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 83 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR C 233 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE C 98 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS C 75 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP C 260 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY C 77 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU C 258 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA C 79 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 256 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP C 254 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 83 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR D 233 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE D 98 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS D 75 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TRP D 260 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY D 77 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU D 258 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA D 79 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR D 256 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 83 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AB9, first strand: chain 'E' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR E 233 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE E 98 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS E 75 " --> pdb=" O TRP E 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP E 260 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY E 77 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU E 258 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA E 79 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR E 256 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 83 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AC4, first strand: chain 'F' and resid 20 through 29 removed outlier: 6.577A pdb=" N THR F 233 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE F 98 " --> pdb=" O THR F 233 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 66 through 70 removed outlier: 6.959A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 75 " --> pdb=" O TRP F 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP F 260 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY F 77 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU F 258 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA F 79 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR F 256 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 83 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 29 removed outlier: 6.578A pdb=" N THR G 233 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE G 98 " --> pdb=" O THR G 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.960A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS G 75 " --> pdb=" O TRP G 260 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP G 260 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY G 77 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 258 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA G 79 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR G 256 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 83 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 174 through 175 763 hydrogen bonds defined for protein. 2121 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: 7.72 Time building geometry restraints manager: 3.63 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: 15921 1.03 - 1.22: 0 1.22 - 1.41: 7260 1.41 - 1.61: 9540 1.61 - 1.80: 98 Bond restraints: 32819 Sorted by residual: bond pdb=" CB PRO F 103 " pdb=" CG PRO F 103 " ideal model delta sigma weight residual 1.506 1.445 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CB PRO A 103 " pdb=" CG PRO A 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.40e+00 bond pdb=" CB PRO G 103 " pdb=" CG PRO G 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.38e+00 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.37e+00 bond pdb=" CB PRO B 103 " pdb=" CG PRO B 103 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.36e+00 ... (remaining 32814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.82: 52918 0.82 - 1.63: 5595 1.63 - 2.45: 397 2.45 - 3.26: 124 3.26 - 4.08: 38 Bond angle restraints: 59072 Sorted by residual: angle pdb=" N SER F 262 " pdb=" CA SER F 262 " pdb=" CB SER F 262 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.04e+00 angle pdb=" N SER G 262 " pdb=" CA SER G 262 " pdb=" CB SER G 262 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.04e+00 angle pdb=" N SER B 262 " pdb=" CA SER B 262 " pdb=" CB SER B 262 " ideal model delta sigma weight residual 114.17 110.75 3.42 1.14e+00 7.69e-01 9.00e+00 angle pdb=" N SER A 262 " pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 114.17 110.78 3.39 1.14e+00 7.69e-01 8.87e+00 angle pdb=" N SER D 262 " pdb=" CA SER D 262 " pdb=" CB SER D 262 " ideal model delta sigma weight residual 114.17 110.78 3.39 1.14e+00 7.69e-01 8.86e+00 ... (remaining 59067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 14722 17.84 - 35.68: 576 35.68 - 53.53: 136 53.53 - 71.37: 29 71.37 - 89.21: 14 Dihedral angle restraints: 15477 sinusoidal: 8274 harmonic: 7203 Sorted by residual: dihedral pdb=" CA PRO G 226 " pdb=" C PRO G 226 " pdb=" N ASP G 227 " pdb=" CA ASP G 227 " ideal model delta harmonic sigma weight residual 180.00 165.99 14.01 0 5.00e+00 4.00e-02 7.85e+00 dihedral pdb=" CA PRO C 226 " pdb=" C PRO C 226 " pdb=" N ASP C 227 " pdb=" CA ASP C 227 " ideal model delta harmonic sigma weight residual 180.00 166.03 13.97 0 5.00e+00 4.00e-02 7.81e+00 dihedral pdb=" CA PRO B 226 " pdb=" C PRO B 226 " pdb=" N ASP B 227 " pdb=" CA ASP B 227 " ideal model delta harmonic sigma weight residual 180.00 166.03 13.97 0 5.00e+00 4.00e-02 7.81e+00 ... (remaining 15474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1188 0.029 - 0.058: 826 0.058 - 0.087: 179 0.087 - 0.116: 166 0.116 - 0.145: 56 Chirality restraints: 2415 Sorted by residual: chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE F 232 " pdb=" N ILE F 232 " pdb=" C ILE F 232 " pdb=" CB ILE F 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2412 not shown) Planarity restraints: 4949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 159 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.29e+00 pdb=" N PRO B 160 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 159 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO F 160 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 160 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 160 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 159 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO C 160 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.016 5.00e-02 4.00e+02 ... (remaining 4946 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 833 2.11 - 2.73: 58933 2.73 - 3.35: 88631 3.35 - 3.98: 123965 3.98 - 4.60: 194743 Nonbonded interactions: 467105 Sorted by model distance: nonbonded pdb=" HG1 THR A 60 " pdb=" OH TYR G 101 " model vdw 1.486 2.450 nonbonded pdb=" OH TYR E 101 " pdb=" HG1 THR F 60 " model vdw 1.488 2.450 nonbonded pdb=" OH TYR B 101 " pdb=" HG1 THR C 60 " model vdw 1.489 2.450 nonbonded pdb=" OH TYR A 101 " pdb=" HG1 THR B 60 " model vdw 1.489 2.450 nonbonded pdb=" OH TYR C 101 " pdb=" HG1 THR D 60 " model vdw 1.489 2.450 ... (remaining 467100 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 and (name N or name CA or name C or name O or name CB o \ r name HA or name HB1 or name HB2 or name HB3)) or resid 2 through 293)) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.760 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.007 0.061 16898 Z= 0.284 Angle : 0.550 4.080 22869 Z= 0.322 Chirality : 0.047 0.145 2415 Planarity : 0.003 0.028 2968 Dihedral : 9.972 89.210 6202 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.39 % Allowed : 2.33 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.21 (0.18), residues: 2037 helix: -4.43 (0.08), residues: 42 sheet: 0.32 (0.16), residues: 1057 loop : -0.35 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.014 0.002 TYR G 65 PHE 0.010 0.001 PHE E 125 TRP 0.005 0.001 TRP C 274 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00675 (16898) covalent geometry : angle 0.54973 (22869) hydrogen bonds : bond 0.11281 ( 742) hydrogen bonds : angle 8.27316 ( 2121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 370 time to evaluate : 0.865 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: A 140 MET cc_start: 0.0822 (tpt) cc_final: -0.0916 (ppp) REVERT: A 170 ILE cc_start: 0.9196 (mm) cc_final: 0.8933 (tp) REVERT: B 140 MET cc_start: 0.1323 (tpt) cc_final: -0.0803 (ppp) REVERT: B 170 ILE cc_start: 0.9186 (mm) cc_final: 0.8885 (tp) REVERT: C 140 MET cc_start: 0.1086 (tpt) cc_final: -0.0645 (ppp) REVERT: C 162 ASP cc_start: 0.7893 (p0) cc_final: 0.7687 (p0) REVERT: C 170 ILE cc_start: 0.9209 (mm) cc_final: 0.8906 (tp) REVERT: D 140 MET cc_start: 0.1541 (tpt) cc_final: -0.0898 (ppp) REVERT: D 170 ILE cc_start: 0.9166 (mm) cc_final: 0.8895 (tp) REVERT: E 140 MET cc_start: 0.1484 (tpt) cc_final: -0.0028 (ppp) REVERT: E 162 ASP cc_start: 0.7894 (p0) cc_final: 0.7687 (p0) REVERT: E 170 ILE cc_start: 0.9104 (mm) cc_final: 0.8859 (tp) REVERT: F 140 MET cc_start: 0.1209 (tpt) cc_final: -0.0470 (ppp) REVERT: F 170 ILE cc_start: 0.9201 (mm) cc_final: 0.8940 (tp) REVERT: G 140 MET cc_start: 0.0599 (tpt) cc_final: -0.0792 (ppp) REVERT: G 162 ASP cc_start: 0.7977 (p0) cc_final: 0.7772 (p0) REVERT: G 170 ILE cc_start: 0.9166 (mm) cc_final: 0.8904 (tp) outliers start: 7 outliers final: 0 residues processed: 377 average time/residue: 0.3907 time to fit residues: 200.4054 Evaluate side-chains 212 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN F 177 GLN F 201 ASN G 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.072541 restraints weight = 87882.760| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.75 r_work: 0.2707 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16898 Z= 0.136 Angle : 0.516 4.738 22869 Z= 0.277 Chirality : 0.047 0.162 2415 Planarity : 0.003 0.045 2968 Dihedral : 4.593 18.607 2219 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.61 % Allowed : 9.69 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.13 (0.19), residues: 2037 helix: -4.39 (0.10), residues: 42 sheet: 0.37 (0.16), residues: 1043 loop : 0.13 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.012 0.001 TYR C 65 PHE 0.006 0.001 PHE A 124 TRP 0.007 0.001 TRP A 260 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00287 (16898) covalent geometry : angle 0.51603 (22869) hydrogen bonds : bond 0.03490 ( 742) hydrogen bonds : angle 6.89144 ( 2121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 0.875 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: A 154 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8940 (mtpp) REVERT: B 158 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8725 (mt-10) REVERT: B 287 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8628 (mp0) REVERT: C 94 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7995 (mm-30) REVERT: C 162 ASP cc_start: 0.8904 (p0) cc_final: 0.8664 (p0) REVERT: C 291 MET cc_start: 0.8270 (ttm) cc_final: 0.8005 (ttm) REVERT: E 154 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8902 (mtmt) REVERT: E 162 ASP cc_start: 0.8935 (p0) cc_final: 0.8715 (p0) REVERT: F 8 LYS cc_start: 0.8870 (tttm) cc_final: 0.8544 (ttpp) REVERT: G 8 LYS cc_start: 0.8890 (tttm) cc_final: 0.8631 (ttpp) REVERT: G 154 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8928 (mtpp) REVERT: G 162 ASP cc_start: 0.8836 (p0) cc_final: 0.8592 (p0) REVERT: G 170 ILE cc_start: 0.9368 (mm) cc_final: 0.9140 (tp) outliers start: 11 outliers final: 10 residues processed: 258 average time/residue: 0.3817 time to fit residues: 135.5388 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 50.0000 chunk 151 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 214 ASN F 177 GLN F 259 HIS G 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.069524 restraints weight = 88937.988| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.61 r_work: 0.2659 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16898 Z= 0.225 Angle : 0.508 5.048 22869 Z= 0.272 Chirality : 0.046 0.147 2415 Planarity : 0.003 0.047 2968 Dihedral : 4.596 22.713 2219 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.05 % Allowed : 10.47 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.07 (0.19), residues: 2037 helix: -4.28 (0.09), residues: 42 sheet: 0.31 (0.16), residues: 1064 loop : 0.11 (0.22), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 66 TYR 0.011 0.001 TYR A 65 PHE 0.007 0.001 PHE E 196 TRP 0.005 0.001 TRP E 187 HIS 0.006 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00488 (16898) covalent geometry : angle 0.50831 (22869) hydrogen bonds : bond 0.03410 ( 742) hydrogen bonds : angle 6.57694 ( 2121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.698 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: A 154 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8831 (mtpp) REVERT: B 94 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 212 ASP cc_start: 0.9105 (t0) cc_final: 0.8832 (t0) REVERT: C 94 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8050 (mm-30) REVERT: C 162 ASP cc_start: 0.8947 (p0) cc_final: 0.8729 (p0) REVERT: C 280 GLU cc_start: 0.8112 (mp0) cc_final: 0.7846 (mp0) REVERT: D 100 ASP cc_start: 0.9329 (t0) cc_final: 0.9013 (t0) REVERT: D 174 MET cc_start: 0.8728 (ttp) cc_final: 0.8443 (tmm) REVERT: E 154 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8892 (mtpp) REVERT: E 162 ASP cc_start: 0.9011 (p0) cc_final: 0.8803 (p0) REVERT: F 8 LYS cc_start: 0.8910 (tttm) cc_final: 0.8581 (ttpp) REVERT: G 162 ASP cc_start: 0.8921 (p0) cc_final: 0.8682 (p0) REVERT: G 280 GLU cc_start: 0.8074 (mp0) cc_final: 0.7847 (mp0) outliers start: 19 outliers final: 18 residues processed: 248 average time/residue: 0.3823 time to fit residues: 130.3910 Evaluate side-chains 233 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 84 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 127 optimal weight: 40.0000 chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 177 GLN C 177 GLN C 214 ASN E 177 GLN F 177 GLN F 259 HIS G 105 ASN G 177 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.069473 restraints weight = 89512.823| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.69 r_work: 0.2640 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16898 Z= 0.194 Angle : 0.486 4.789 22869 Z= 0.260 Chirality : 0.046 0.152 2415 Planarity : 0.003 0.049 2968 Dihedral : 4.502 20.649 2219 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.78 % Allowed : 11.30 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.09 (0.19), residues: 2037 helix: -3.95 (0.12), residues: 42 sheet: 0.33 (0.16), residues: 1064 loop : 0.10 (0.22), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 66 TYR 0.011 0.001 TYR F 65 PHE 0.011 0.001 PHE F 196 TRP 0.004 0.001 TRP B 179 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00413 (16898) covalent geometry : angle 0.48641 (22869) hydrogen bonds : bond 0.03173 ( 742) hydrogen bonds : angle 6.35614 ( 2121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 1.016 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: A 154 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8885 (mtpp) REVERT: B 170 ILE cc_start: 0.9254 (tp) cc_final: 0.8936 (pt) REVERT: B 280 GLU cc_start: 0.8077 (mp0) cc_final: 0.7673 (mp0) REVERT: C 94 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7980 (mm-30) REVERT: C 154 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8820 (mtpp) REVERT: C 162 ASP cc_start: 0.8964 (p0) cc_final: 0.8729 (p0) REVERT: C 234 MET cc_start: 0.8794 (tpp) cc_final: 0.7900 (tpp) REVERT: C 280 GLU cc_start: 0.8106 (mp0) cc_final: 0.7730 (mp0) REVERT: D 8 LYS cc_start: 0.8953 (tttm) cc_final: 0.8670 (ttpp) REVERT: D 100 ASP cc_start: 0.9314 (t0) cc_final: 0.9003 (t0) REVERT: D 174 MET cc_start: 0.8691 (ttp) cc_final: 0.8459 (tmm) REVERT: E 162 ASP cc_start: 0.9029 (p0) cc_final: 0.8797 (p0) REVERT: E 280 GLU cc_start: 0.7921 (mp0) cc_final: 0.7692 (mp0) REVERT: F 8 LYS cc_start: 0.8929 (tttm) cc_final: 0.8624 (ttpp) REVERT: F 154 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8880 (mtpp) REVERT: G 8 LYS cc_start: 0.8904 (tttm) cc_final: 0.8650 (ttpp) REVERT: G 162 ASP cc_start: 0.8999 (p0) cc_final: 0.8759 (p0) outliers start: 14 outliers final: 14 residues processed: 246 average time/residue: 0.3899 time to fit residues: 131.0312 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 130 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN B 177 GLN C 177 GLN C 214 ASN E 177 GLN F 177 GLN G 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.065740 restraints weight = 89866.092| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.68 r_work: 0.2559 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16898 Z= 0.294 Angle : 0.521 4.416 22869 Z= 0.281 Chirality : 0.046 0.141 2415 Planarity : 0.004 0.067 2968 Dihedral : 4.667 27.737 2219 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 11.02 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.08 (0.19), residues: 2037 helix: -2.77 (0.36), residues: 42 sheet: 0.30 (0.16), residues: 1043 loop : -0.20 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.012 0.001 TYR G 65 PHE 0.009 0.001 PHE G 196 TRP 0.005 0.001 TRP E 187 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00631 (16898) covalent geometry : angle 0.52068 (22869) hydrogen bonds : bond 0.03403 ( 742) hydrogen bonds : angle 6.32608 ( 2121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.903 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: A 154 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8774 (mtpp) REVERT: B 280 GLU cc_start: 0.8049 (mp0) cc_final: 0.7655 (mp0) REVERT: C 94 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8017 (mm-30) REVERT: C 154 LYS cc_start: 0.9127 (mtpp) cc_final: 0.8841 (mtpp) REVERT: C 162 ASP cc_start: 0.9061 (p0) cc_final: 0.8847 (p0) REVERT: C 280 GLU cc_start: 0.8036 (mp0) cc_final: 0.7555 (mp0) REVERT: D 92 ASP cc_start: 0.9069 (p0) cc_final: 0.8834 (p0) REVERT: E 280 GLU cc_start: 0.7921 (mp0) cc_final: 0.7461 (mp0) REVERT: F 8 LYS cc_start: 0.8998 (tttm) cc_final: 0.8687 (ttpp) REVERT: F 154 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8912 (mtpp) REVERT: G 280 GLU cc_start: 0.8049 (mp0) cc_final: 0.7722 (mp0) outliers start: 30 outliers final: 28 residues processed: 233 average time/residue: 0.4001 time to fit residues: 127.7595 Evaluate side-chains 233 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 272 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.8980 chunk 156 optimal weight: 40.0000 chunk 154 optimal weight: 4.9990 chunk 145 optimal weight: 0.0070 chunk 147 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 127 optimal weight: 40.0000 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 177 GLN C 177 GLN C 214 ASN D 177 GLN E 177 GLN F 105 ASN F 177 GLN G 177 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.066823 restraints weight = 89362.717| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.69 r_work: 0.2585 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16898 Z= 0.209 Angle : 0.488 6.538 22869 Z= 0.262 Chirality : 0.046 0.148 2415 Planarity : 0.003 0.056 2968 Dihedral : 4.555 24.514 2219 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.44 % Allowed : 11.74 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.02 (0.19), residues: 2037 helix: -2.10 (0.49), residues: 42 sheet: 0.31 (0.16), residues: 1057 loop : -0.17 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 66 TYR 0.011 0.001 TYR E 65 PHE 0.009 0.001 PHE B 196 TRP 0.004 0.001 TRP D 260 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00442 (16898) covalent geometry : angle 0.48816 (22869) hydrogen bonds : bond 0.03142 ( 742) hydrogen bonds : angle 6.19555 ( 2121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.844 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: A 154 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8781 (mtpp) REVERT: B 280 GLU cc_start: 0.8084 (mp0) cc_final: 0.7712 (mp0) REVERT: C 94 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8000 (mm-30) REVERT: C 154 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8828 (mtpp) REVERT: C 162 ASP cc_start: 0.9048 (p0) cc_final: 0.8789 (p0) REVERT: C 280 GLU cc_start: 0.8086 (mp0) cc_final: 0.7593 (mp0) REVERT: E 280 GLU cc_start: 0.7901 (mp0) cc_final: 0.7525 (mp0) REVERT: F 8 LYS cc_start: 0.8982 (tttm) cc_final: 0.8699 (ttpp) REVERT: F 154 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8951 (mtpp) REVERT: G 92 ASP cc_start: 0.8974 (p0) cc_final: 0.8579 (t0) REVERT: G 280 GLU cc_start: 0.8077 (mp0) cc_final: 0.7795 (mp0) outliers start: 26 outliers final: 26 residues processed: 236 average time/residue: 0.3859 time to fit residues: 125.2706 Evaluate side-chains 239 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 272 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 126 optimal weight: 4.9990 chunk 192 optimal weight: 0.0670 chunk 151 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 177 GLN C 177 GLN C 214 ASN D 177 GLN E 177 GLN F 177 GLN G 177 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.065646 restraints weight = 90133.427| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.69 r_work: 0.2566 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16898 Z= 0.273 Angle : 0.510 5.051 22869 Z= 0.275 Chirality : 0.046 0.144 2415 Planarity : 0.003 0.052 2968 Dihedral : 4.615 27.018 2219 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.55 % Allowed : 11.52 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.23 (0.19), residues: 2037 helix: -0.74 (0.67), residues: 42 sheet: 0.16 (0.16), residues: 1043 loop : -0.35 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 66 TYR 0.012 0.001 TYR E 65 PHE 0.011 0.001 PHE F 196 TRP 0.004 0.001 TRP B 187 HIS 0.003 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00583 (16898) covalent geometry : angle 0.50959 (22869) hydrogen bonds : bond 0.03281 ( 742) hydrogen bonds : angle 6.18126 ( 2121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.801 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: A 154 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8802 (mtpp) REVERT: B 92 ASP cc_start: 0.9009 (p0) cc_final: 0.8649 (t0) REVERT: B 280 GLU cc_start: 0.8073 (mp0) cc_final: 0.7814 (mp0) REVERT: C 92 ASP cc_start: 0.9078 (p0) cc_final: 0.8665 (t0) REVERT: C 94 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7996 (mm-30) REVERT: C 154 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8840 (mtpp) REVERT: C 162 ASP cc_start: 0.9102 (p0) cc_final: 0.8846 (p0) REVERT: C 280 GLU cc_start: 0.8082 (mp0) cc_final: 0.7540 (mp0) REVERT: D 92 ASP cc_start: 0.9052 (p0) cc_final: 0.8830 (p0) REVERT: E 280 GLU cc_start: 0.7902 (mp0) cc_final: 0.7531 (mp0) REVERT: F 8 LYS cc_start: 0.8997 (tttm) cc_final: 0.8691 (ttpp) REVERT: F 154 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8940 (mtpp) REVERT: G 92 ASP cc_start: 0.8970 (p0) cc_final: 0.8662 (t0) REVERT: G 280 GLU cc_start: 0.8048 (mp0) cc_final: 0.7744 (mp0) outliers start: 28 outliers final: 27 residues processed: 234 average time/residue: 0.3942 time to fit residues: 127.2994 Evaluate side-chains 237 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 272 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 169 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 177 GLN C 177 GLN D 177 GLN F 177 GLN G 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.066072 restraints weight = 89405.637| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.71 r_work: 0.2578 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16898 Z= 0.231 Angle : 0.494 4.831 22869 Z= 0.266 Chirality : 0.046 0.144 2415 Planarity : 0.003 0.049 2968 Dihedral : 4.547 24.201 2219 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.50 % Allowed : 12.13 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.16 (0.19), residues: 2037 helix: -0.52 (0.69), residues: 42 sheet: 0.18 (0.16), residues: 1057 loop : -0.30 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 66 TYR 0.012 0.001 TYR E 65 PHE 0.011 0.001 PHE F 196 TRP 0.004 0.001 TRP D 260 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00491 (16898) covalent geometry : angle 0.49439 (22869) hydrogen bonds : bond 0.03126 ( 742) hydrogen bonds : angle 6.10338 ( 2121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.917 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: A 154 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8782 (mtpp) REVERT: B 92 ASP cc_start: 0.8974 (p0) cc_final: 0.8651 (t0) REVERT: B 280 GLU cc_start: 0.8117 (mp0) cc_final: 0.7801 (mp0) REVERT: C 92 ASP cc_start: 0.9022 (p0) cc_final: 0.8662 (t0) REVERT: C 94 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 154 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8820 (mtpp) REVERT: C 162 ASP cc_start: 0.9105 (p0) cc_final: 0.8835 (p0) REVERT: C 280 GLU cc_start: 0.8058 (mp0) cc_final: 0.7601 (mp0) REVERT: D 8 LYS cc_start: 0.9012 (tttm) cc_final: 0.8736 (ttpp) REVERT: D 92 ASP cc_start: 0.9048 (p0) cc_final: 0.8846 (p0) REVERT: F 8 LYS cc_start: 0.8998 (tttm) cc_final: 0.8696 (ttpp) REVERT: F 154 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8936 (mtpp) REVERT: G 92 ASP cc_start: 0.8951 (p0) cc_final: 0.8640 (t0) REVERT: G 280 GLU cc_start: 0.8011 (mp0) cc_final: 0.7763 (mp0) outliers start: 27 outliers final: 27 residues processed: 233 average time/residue: 0.3828 time to fit residues: 122.2426 Evaluate side-chains 239 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 272 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 127 optimal weight: 40.0000 chunk 77 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN C 214 ASN E 177 GLN F 177 GLN G 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.068507 restraints weight = 88296.279| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.72 r_work: 0.2618 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16898 Z= 0.118 Angle : 0.463 4.619 22869 Z= 0.248 Chirality : 0.046 0.147 2415 Planarity : 0.003 0.070 2968 Dihedral : 4.352 18.425 2219 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.66 % Allowed : 13.07 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.03 (0.19), residues: 2037 helix: -0.24 (0.71), residues: 42 sheet: 0.25 (0.16), residues: 1057 loop : -0.19 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 56 TYR 0.010 0.001 TYR E 65 PHE 0.012 0.001 PHE F 196 TRP 0.005 0.001 TRP D 260 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00249 (16898) covalent geometry : angle 0.46342 (22869) hydrogen bonds : bond 0.02753 ( 742) hydrogen bonds : angle 5.93080 ( 2121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.972 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: A 154 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8726 (mtpp) REVERT: B 92 ASP cc_start: 0.8917 (p0) cc_final: 0.8629 (t0) REVERT: B 280 GLU cc_start: 0.8174 (mp0) cc_final: 0.7749 (mp0) REVERT: C 92 ASP cc_start: 0.9007 (p0) cc_final: 0.8623 (t0) REVERT: C 94 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 154 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8811 (mtpp) REVERT: C 162 ASP cc_start: 0.9028 (p0) cc_final: 0.8750 (p0) REVERT: C 280 GLU cc_start: 0.8102 (mp0) cc_final: 0.7718 (mp0) REVERT: D 8 LYS cc_start: 0.8995 (tttm) cc_final: 0.8726 (ttpp) REVERT: D 100 ASP cc_start: 0.9252 (t0) cc_final: 0.8925 (t0) REVERT: E 152 ASP cc_start: 0.8920 (m-30) cc_final: 0.8523 (p0) REVERT: E 259 HIS cc_start: 0.7433 (m170) cc_final: 0.7189 (m-70) REVERT: F 8 LYS cc_start: 0.8977 (tttm) cc_final: 0.8721 (ttpp) REVERT: F 154 LYS cc_start: 0.9147 (mtmt) cc_final: 0.8907 (mtpp) REVERT: G 8 LYS cc_start: 0.8935 (tttm) cc_final: 0.8715 (ttpp) REVERT: G 92 ASP cc_start: 0.8891 (p0) cc_final: 0.8582 (t0) REVERT: G 280 GLU cc_start: 0.8006 (mp0) cc_final: 0.7793 (mp0) outliers start: 12 outliers final: 8 residues processed: 247 average time/residue: 0.3773 time to fit residues: 127.8444 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 226 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 161 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS C 214 ASN F 177 GLN G 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.066832 restraints weight = 89429.011| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.72 r_work: 0.2585 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16898 Z= 0.212 Angle : 0.492 9.106 22869 Z= 0.263 Chirality : 0.045 0.143 2415 Planarity : 0.004 0.077 2968 Dihedral : 4.414 23.650 2219 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.44 % Allowed : 13.51 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.18 (0.19), residues: 2037 helix: 0.16 (0.76), residues: 42 sheet: 0.12 (0.16), residues: 1071 loop : -0.29 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 66 TYR 0.012 0.001 TYR A 65 PHE 0.012 0.001 PHE D 196 TRP 0.003 0.001 TRP D 187 HIS 0.003 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00453 (16898) covalent geometry : angle 0.49211 (22869) hydrogen bonds : bond 0.02992 ( 742) hydrogen bonds : angle 5.95450 ( 2121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.840 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: A 154 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8749 (mtpp) REVERT: B 92 ASP cc_start: 0.8944 (p0) cc_final: 0.8637 (t0) REVERT: B 156 ILE cc_start: 0.9435 (mt) cc_final: 0.9194 (mm) REVERT: B 280 GLU cc_start: 0.8158 (mp0) cc_final: 0.7805 (mp0) REVERT: C 92 ASP cc_start: 0.9025 (p0) cc_final: 0.8674 (t0) REVERT: C 94 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 154 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8847 (mtpp) REVERT: C 162 ASP cc_start: 0.9085 (p0) cc_final: 0.8818 (p0) REVERT: C 280 GLU cc_start: 0.8101 (mp0) cc_final: 0.7586 (mp0) REVERT: D 8 LYS cc_start: 0.9030 (tttm) cc_final: 0.8759 (ttpp) REVERT: D 100 ASP cc_start: 0.9277 (t0) cc_final: 0.8931 (t0) REVERT: E 152 ASP cc_start: 0.8904 (m-30) cc_final: 0.8527 (p0) REVERT: E 259 HIS cc_start: 0.7448 (m170) cc_final: 0.7217 (m-70) REVERT: F 8 LYS cc_start: 0.8986 (tttm) cc_final: 0.8728 (ttpp) REVERT: F 154 LYS cc_start: 0.9110 (mtmt) cc_final: 0.8866 (mtpp) REVERT: F 237 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9251 (mmtm) REVERT: G 8 LYS cc_start: 0.8947 (tttm) cc_final: 0.8720 (ttpp) REVERT: G 92 ASP cc_start: 0.8937 (p0) cc_final: 0.8654 (t0) REVERT: G 280 GLU cc_start: 0.8060 (mp0) cc_final: 0.7799 (mp0) outliers start: 8 outliers final: 8 residues processed: 226 average time/residue: 0.3911 time to fit residues: 120.2355 Evaluate side-chains 230 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 183 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 177 GLN E 177 GLN F 177 GLN G 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.066808 restraints weight = 89410.631| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.72 r_work: 0.2583 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16898 Z= 0.206 Angle : 0.486 9.879 22869 Z= 0.261 Chirality : 0.045 0.143 2415 Planarity : 0.004 0.066 2968 Dihedral : 4.414 22.376 2219 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.55 % Allowed : 12.96 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.17 (0.19), residues: 2037 helix: 0.27 (0.76), residues: 42 sheet: 0.12 (0.16), residues: 1064 loop : -0.26 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 66 TYR 0.012 0.001 TYR A 65 PHE 0.012 0.001 PHE A 196 TRP 0.003 0.001 TRP D 260 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00439 (16898) covalent geometry : angle 0.48593 (22869) hydrogen bonds : bond 0.02952 ( 742) hydrogen bonds : angle 5.92726 ( 2121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6592.23 seconds wall clock time: 112 minutes 54.09 seconds (6774.09 seconds total)