Starting phenix.real_space_refine (version: dev) on Wed Apr 6 15:56:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/04_2022/6qd0_4515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/04_2022/6qd0_4515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/04_2022/6qd0_4515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/04_2022/6qd0_4515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/04_2022/6qd0_4515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/04_2022/6qd0_4515.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "D" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.21, per 1000 atoms: 0.47 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 102.7, 93.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 44 16.00 O 1844 8.00 N 1820 7.00 C 6936 6.00 H 11100 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 19.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 65.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.515A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.546A pdb=" N ALA A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.807A pdb=" N ILE A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 61 removed outlier: 3.666A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.711A pdb=" N ILE A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.688A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 103 through 104 No H-bonds generated for 'chain 'A' and resid 103 through 104' Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.164A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 152 removed outlier: 4.003A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.651A pdb=" N TRP A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 225 removed outlier: 3.560A pdb=" N ARG A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.918A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.514A pdb=" N LEU B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.545A pdb=" N ALA B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.807A pdb=" N ILE B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 61 removed outlier: 3.666A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 92 removed outlier: 4.712A pdb=" N ILE B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 3.688A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 103 through 104 No H-bonds generated for 'chain 'B' and resid 103 through 104' Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.163A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 152 removed outlier: 4.002A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.653A pdb=" N TRP B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 225 removed outlier: 3.559A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N MET B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.918A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.514A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.545A pdb=" N ALA C 24 " --> pdb=" O PRO C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.807A pdb=" N ILE C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 61 removed outlier: 3.665A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 4.711A pdb=" N ILE C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.688A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 103 through 104 No H-bonds generated for 'chain 'C' and resid 103 through 104' Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.163A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 152 removed outlier: 4.003A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.652A pdb=" N TRP C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 225 removed outlier: 3.560A pdb=" N ARG C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.918A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 removed outlier: 3.515A pdb=" N LEU D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.546A pdb=" N ALA D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.808A pdb=" N ILE D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 61 removed outlier: 3.666A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 removed outlier: 4.711A pdb=" N ILE D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.687A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 104 No H-bonds generated for 'chain 'D' and resid 103 through 104' Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.163A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 152 removed outlier: 4.003A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.653A pdb=" N TRP D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 225 removed outlier: 3.559A pdb=" N ARG D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 removed outlier: 4.014A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.919A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 320 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 275 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 320 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 275 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.588A pdb=" N VAL A 311 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 310 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 320 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 275 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 320 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 275 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 263 removed outlier: 6.588A pdb=" N VAL B 311 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR B 310 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 320 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 275 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 320 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 275 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 261 through 263 removed outlier: 6.588A pdb=" N VAL C 311 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 310 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 320 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL D 275 " --> pdb=" O LEU D 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 253 through 256 removed outlier: 4.045A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 320 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL D 275 " --> pdb=" O LEU D 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 261 through 263 removed outlier: 6.587A pdb=" N VAL D 311 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR D 310 " --> pdb=" O ALA D 283 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 19.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11088 1.03 - 1.22: 12 1.22 - 1.42: 4343 1.42 - 1.61: 6461 1.61 - 1.80: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" CB LEU B 106 " pdb=" HB3 LEU B 106 " ideal model delta sigma weight residual 0.970 1.012 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" CB LEU A 106 " pdb=" HB3 LEU A 106 " ideal model delta sigma weight residual 0.970 1.012 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" CB LEU D 106 " pdb=" HB3 LEU D 106 " ideal model delta sigma weight residual 0.970 1.012 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" CB LEU C 106 " pdb=" HB3 LEU C 106 " ideal model delta sigma weight residual 0.970 1.011 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" CZ ARG A 220 " pdb=" NH2 ARG A 220 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.81e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.91: 330 104.91 - 112.23: 25625 112.23 - 119.54: 5786 119.54 - 126.85: 8027 126.85 - 134.17: 172 Bond angle restraints: 39940 Sorted by residual: angle pdb=" CG HIS B 323 " pdb=" CB HIS B 323 " pdb=" HB3 HIS B 323 " ideal model delta sigma weight residual 108.00 98.97 9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" N ALA B 294 " pdb=" CA ALA B 294 " pdb=" C ALA B 294 " ideal model delta sigma weight residual 108.45 112.19 -3.74 1.26e+00 6.30e-01 8.80e+00 angle pdb=" N ALA A 294 " pdb=" CA ALA A 294 " pdb=" C ALA A 294 " ideal model delta sigma weight residual 108.45 112.18 -3.73 1.26e+00 6.30e-01 8.74e+00 angle pdb=" N ALA C 294 " pdb=" CA ALA C 294 " pdb=" C ALA C 294 " ideal model delta sigma weight residual 108.45 112.16 -3.71 1.26e+00 6.30e-01 8.66e+00 angle pdb=" N ALA D 294 " pdb=" CA ALA D 294 " pdb=" C ALA D 294 " ideal model delta sigma weight residual 108.45 112.14 -3.69 1.26e+00 6.30e-01 8.58e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 8130 15.47 - 30.93: 496 30.93 - 46.40: 38 46.40 - 61.87: 12 61.87 - 77.34: 8 Dihedral angle restraints: 8684 sinusoidal: 4000 harmonic: 4684 Sorted by residual: dihedral pdb=" CA ASN D 226 " pdb=" C ASN D 226 " pdb=" N TRP D 227 " pdb=" CA TRP D 227 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASN A 226 " pdb=" C ASN A 226 " pdb=" N TRP A 227 " pdb=" CA TRP A 227 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN B 226 " pdb=" C ASN B 226 " pdb=" N TRP B 227 " pdb=" CA TRP B 227 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 8681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 879 0.029 - 0.057: 531 0.057 - 0.086: 225 0.086 - 0.115: 105 0.115 - 0.143: 44 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA VAL A 288 " pdb=" N VAL A 288 " pdb=" C VAL A 288 " pdb=" CB VAL A 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA VAL D 288 " pdb=" N VAL D 288 " pdb=" C VAL D 288 " pdb=" CB VAL D 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL B 288 " pdb=" N VAL B 288 " pdb=" C VAL B 288 " pdb=" CB VAL B 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" N ALA A 325 " -0.040 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.010 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C LEU A 210 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 210 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 211 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LEU D 210 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU D 210 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 211 " -0.013 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.35: 8011 2.35 - 3.05: 64371 3.05 - 3.75: 74419 3.75 - 4.44: 116971 4.44 - 5.14: 176277 Nonbonded interactions: 440049 Sorted by model distance: nonbonded pdb=" H GLY C 259 " pdb=" O ALA C 313 " model vdw 1.654 1.850 nonbonded pdb=" H GLY D 259 " pdb=" O ALA D 313 " model vdw 1.655 1.850 nonbonded pdb=" H GLY A 259 " pdb=" O ALA A 313 " model vdw 1.655 1.850 nonbonded pdb=" H GLY B 259 " pdb=" O ALA B 313 " model vdw 1.655 1.850 nonbonded pdb=" O PRO A 234 " pdb="HE22 GLN A 237 " model vdw 1.661 1.850 ... (remaining 440044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 355) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 44 5.16 5 C 6936 2.51 5 N 1820 2.21 5 O 1844 1.98 5 H 11100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.310 Extract box with map and model: 2.340 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.180 Process input model: 72.240 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.047 10880 Z= 0.584 Angle : 1.026 8.406 14852 Z= 0.568 Chirality : 0.048 0.143 1784 Planarity : 0.007 0.046 1872 Dihedral : 9.680 77.336 3844 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.19), residues: 1412 helix: -4.10 (0.11), residues: 660 sheet: -4.42 (0.41), residues: 40 loop : -2.28 (0.25), residues: 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.5301 time to fit residues: 299.1862 Evaluate side-chains 259 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN C 216 GLN D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10880 Z= 0.232 Angle : 0.715 6.769 14852 Z= 0.388 Chirality : 0.042 0.150 1784 Planarity : 0.007 0.088 1872 Dihedral : 6.688 24.121 1536 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.21), residues: 1412 helix: -2.30 (0.16), residues: 680 sheet: -3.79 (0.56), residues: 40 loop : -2.36 (0.25), residues: 692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4463 time to fit residues: 202.4873 Evaluate side-chains 249 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 40.0000 chunk 39 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10880 Z= 0.230 Angle : 0.655 6.022 14852 Z= 0.357 Chirality : 0.041 0.139 1784 Planarity : 0.006 0.084 1872 Dihedral : 6.054 20.885 1536 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.22), residues: 1412 helix: -1.37 (0.18), residues: 704 sheet: -3.31 (0.65), residues: 40 loop : -2.39 (0.25), residues: 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.4421 time to fit residues: 206.4029 Evaluate side-chains 219 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 chunk 66 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 135 optimal weight: 50.0000 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10880 Z= 0.213 Angle : 0.619 5.629 14852 Z= 0.335 Chirality : 0.040 0.140 1784 Planarity : 0.006 0.096 1872 Dihedral : 5.728 21.866 1536 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.22), residues: 1412 helix: -1.31 (0.18), residues: 732 sheet: -3.16 (0.67), residues: 40 loop : -2.22 (0.27), residues: 640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.4471 time to fit residues: 195.5967 Evaluate side-chains 222 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 226 ASN B 216 GLN C 226 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 10880 Z= 0.264 Angle : 0.656 8.006 14852 Z= 0.356 Chirality : 0.041 0.147 1784 Planarity : 0.006 0.098 1872 Dihedral : 5.690 20.153 1536 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1412 helix: -1.47 (0.17), residues: 764 sheet: -3.23 (0.63), residues: 40 loop : -2.36 (0.27), residues: 608 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4514 time to fit residues: 180.2281 Evaluate side-chains 226 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 10880 Z= 0.238 Angle : 0.613 7.449 14852 Z= 0.331 Chirality : 0.040 0.142 1784 Planarity : 0.009 0.226 1872 Dihedral : 5.528 22.372 1536 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.22), residues: 1412 helix: -1.18 (0.18), residues: 732 sheet: -3.05 (0.65), residues: 40 loop : -2.06 (0.27), residues: 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.4463 time to fit residues: 181.7138 Evaluate side-chains 225 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 83 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 10880 Z= 0.198 Angle : 0.580 5.239 14852 Z= 0.309 Chirality : 0.040 0.132 1784 Planarity : 0.006 0.104 1872 Dihedral : 5.155 18.630 1536 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1412 helix: -1.05 (0.18), residues: 748 sheet: -2.53 (0.68), residues: 40 loop : -2.11 (0.28), residues: 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.4469 time to fit residues: 182.4091 Evaluate side-chains 236 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 10880 Z= 0.198 Angle : 0.577 6.481 14852 Z= 0.309 Chirality : 0.039 0.144 1784 Planarity : 0.006 0.116 1872 Dihedral : 4.976 18.376 1536 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1412 helix: -0.82 (0.18), residues: 764 sheet: -2.19 (0.71), residues: 40 loop : -2.15 (0.27), residues: 608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.4733 time to fit residues: 193.7699 Evaluate side-chains 243 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 10880 Z= 0.199 Angle : 0.577 6.614 14852 Z= 0.307 Chirality : 0.039 0.132 1784 Planarity : 0.006 0.096 1872 Dihedral : 4.906 18.020 1536 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.23), residues: 1412 helix: -0.62 (0.18), residues: 740 sheet: -1.92 (0.74), residues: 40 loop : -2.08 (0.27), residues: 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.4417 time to fit residues: 179.6903 Evaluate side-chains 238 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 overall best weight: 2.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 10880 Z= 0.172 Angle : 0.561 7.961 14852 Z= 0.293 Chirality : 0.039 0.121 1784 Planarity : 0.006 0.088 1872 Dihedral : 4.769 17.650 1536 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.23), residues: 1412 helix: -0.30 (0.19), residues: 740 sheet: -1.53 (0.79), residues: 40 loop : -1.98 (0.27), residues: 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.4404 time to fit residues: 179.9682 Evaluate side-chains 248 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.170701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.135867 restraints weight = 69883.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.141116 restraints weight = 37279.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144650 restraints weight = 23974.265| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.118 10880 Z= 0.230 Angle : 0.605 10.865 14852 Z= 0.328 Chirality : 0.039 0.191 1784 Planarity : 0.007 0.135 1872 Dihedral : 4.825 17.411 1536 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.23), residues: 1412 helix: -0.31 (0.19), residues: 760 sheet: -1.65 (0.78), residues: 40 loop : -1.93 (0.28), residues: 612 =============================================================================== Job complete usr+sys time: 4317.82 seconds wall clock time: 77 minutes 22.03 seconds (4642.03 seconds total)