Starting phenix.real_space_refine (version: dev) on Fri Apr 8 04:54:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/04_2022/7o1q_12696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/04_2022/7o1q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/04_2022/7o1q_12696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/04_2022/7o1q_12696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/04_2022/7o1q_12696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/04_2022/7o1q_12696.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} 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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} 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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} 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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} 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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} 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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} 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: {'PTRANS': 8, 'TRANS': 283, 'PCIS': 1} Time building chain proxies: 14.03, per 1000 atoms: 0.43 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 - 3.50 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: 25.39 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 0.93 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: 12.09 Time building geometry restraints manager: 26.29 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: 98.82 - 105.86: 276 105.86 - 112.90: 37654 112.90 - 119.94: 8699 119.94 - 126.98: 12204 126.98 - 134.02: 239 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: 12748 17.84 - 35.68: 443 35.68 - 53.53: 31 53.53 - 71.37: 8 71.37 - 89.21: 14 Dihedral angle restraints: 13244 sinusoidal: 6041 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 13241 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 1.850 nonbonded pdb=" OH TYR E 101 " pdb=" HG1 THR F 60 " model vdw 1.488 1.850 nonbonded pdb=" OH TYR B 101 " pdb=" HG1 THR C 60 " model vdw 1.489 1.850 nonbonded pdb=" OH TYR A 101 " pdb=" HG1 THR B 60 " model vdw 1.489 1.850 nonbonded pdb=" OH TYR C 101 " pdb=" HG1 THR D 60 " model vdw 1.489 1.850 ... (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 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 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. 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: 0.380 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: 0.470 Extract box with map and model: 4.680 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.270 Process input model: 93.300 Find NCS groups from input model: 1.480 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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= 0.434 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -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 *********************** 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 fitting. rotamer outliers: 7 poor density : 370 time to evaluate : 2.968 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 outliers start: 7 outliers final: 0 residues processed: 377 average time/residue: 0.7860 time to fit residues: 414.5105 Evaluate side-chains 206 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 16898 Z= 0.146 Angle : 0.496 4.421 22869 Z= 0.266 Chirality : 0.047 0.160 2415 Planarity : 0.003 0.049 2968 Dihedral : 4.608 19.779 2219 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.24 (0.19), residues: 2037 helix: -4.34 (0.08), residues: 42 sheet: 0.50 (0.16), residues: 1057 loop : 0.13 (0.21), residues: 938 *********************** 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 256 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 3.051 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 outliers start: 9 outliers final: 8 residues processed: 254 average time/residue: 0.7889 time to fit residues: 287.8150 Evaluate side-chains 222 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 214 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3836 time to fit residues: 9.1491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS B 105 ASN B 172 ASN C 259 HIS D 259 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 259 HIS F 259 HIS G 259 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 16898 Z= 0.397 Angle : 0.534 4.225 22869 Z= 0.287 Chirality : 0.046 0.144 2415 Planarity : 0.003 0.045 2968 Dihedral : 4.984 38.156 2219 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.00 (0.19), residues: 2037 helix: -2.67 (0.46), residues: 42 sheet: 0.35 (0.16), residues: 1050 loop : -0.15 (0.20), residues: 945 *********************** 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 224 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 2.651 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 outliers start: 21 outliers final: 21 residues processed: 215 average time/residue: 0.7922 time to fit residues: 239.6100 Evaluate side-chains 213 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 2.846 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3504 time to fit residues: 17.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 50.0000 chunk 196 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 16898 Z= 0.136 Angle : 0.473 4.472 22869 Z= 0.250 Chirality : 0.046 0.144 2415 Planarity : 0.003 0.049 2968 Dihedral : 4.514 28.850 2219 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.29 (0.19), residues: 2037 helix: -3.32 (0.26), residues: 42 sheet: 0.50 (0.16), residues: 1064 loop : 0.14 (0.21), residues: 931 *********************** 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 237 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 2.834 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 outliers start: 3 outliers final: 2 residues processed: 237 average time/residue: 0.7730 time to fit residues: 258.5266 Evaluate side-chains 213 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3429 time to fit residues: 4.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 50.0000 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS B 259 HIS D 172 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 16898 Z= 0.448 Angle : 0.540 5.334 22869 Z= 0.290 Chirality : 0.046 0.139 2415 Planarity : 0.003 0.061 2968 Dihedral : 4.889 37.395 2219 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.03 (0.19), residues: 2037 helix: -0.71 (0.74), residues: 42 sheet: 0.40 (0.16), residues: 1043 loop : -0.27 (0.20), residues: 952 *********************** 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 226 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 30 residues processed: 210 average time/residue: 0.7951 time to fit residues: 232.6336 Evaluate side-chains 219 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3408 time to fit residues: 22.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 16898 Z= 0.136 Angle : 0.469 4.111 22869 Z= 0.248 Chirality : 0.046 0.153 2415 Planarity : 0.003 0.047 2968 Dihedral : 4.436 26.373 2219 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.29 (0.19), residues: 2037 helix: -1.11 (0.57), residues: 42 sheet: 0.53 (0.16), residues: 1050 loop : -0.01 (0.21), residues: 945 *********************** 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 215 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.804 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 outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.7790 time to fit residues: 235.2637 Evaluate side-chains 206 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 HIS D 259 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3228 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= 0.318 Angle : 0.493 4.953 22869 Z= 0.263 Chirality : 0.045 0.143 2415 Planarity : 0.003 0.074 2968 Dihedral : 4.600 30.044 2219 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.22 (0.19), residues: 2037 helix: 0.49 (0.82), residues: 42 sheet: 0.48 (0.16), residues: 1050 loop : -0.15 (0.20), residues: 945 *********************** 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 199 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 196 average time/residue: 0.8094 time to fit residues: 220.8657 Evaluate side-chains 198 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3237 time to fit residues: 5.7723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 16898 Z= 0.330 Angle : 0.500 4.371 22869 Z= 0.268 Chirality : 0.045 0.142 2415 Planarity : 0.003 0.065 2968 Dihedral : 4.621 28.484 2219 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.12 (0.19), residues: 2037 helix: 0.64 (0.78), residues: 42 sheet: 0.43 (0.16), residues: 1050 loop : -0.25 (0.20), residues: 945 *********************** 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 201 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.8005 time to fit residues: 224.5104 Evaluate side-chains 196 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3211 time to fit residues: 3.7414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 50.0000 chunk 171 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 16898 Z= 0.300 Angle : 0.489 4.480 22869 Z= 0.262 Chirality : 0.045 0.142 2415 Planarity : 0.003 0.071 2968 Dihedral : 4.593 26.760 2219 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.12 (0.19), residues: 2037 helix: 1.36 (0.89), residues: 42 sheet: 0.41 (0.16), residues: 1050 loop : -0.26 (0.20), residues: 945 *********************** 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 203 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 2.664 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 outliers start: 4 outliers final: 4 residues processed: 199 average time/residue: 0.7934 time to fit residues: 221.8712 Evaluate side-chains 201 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3162 time to fit residues: 5.6572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 186 optimal weight: 30.0000 chunk 161 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 50.0000 chunk 127 optimal weight: 40.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN C 17 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 16898 Z= 0.133 Angle : 0.468 9.054 22869 Z= 0.247 Chirality : 0.046 0.148 2415 Planarity : 0.003 0.053 2968 Dihedral : 4.301 18.334 2219 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.36 (0.19), residues: 2037 helix: 1.12 (0.83), residues: 42 sheet: 0.57 (0.16), residues: 1050 loop : -0.08 (0.21), residues: 945 ********************** 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 221 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.621 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 outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.7551 time to fit residues: 237.3877 Evaluate side-chains 210 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.860 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3442 time to fit residues: 4.2428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.069277 restraints weight = 89688.684| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.62 r_work: 0.2792 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work: 0.2762 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work: 0.2745 rms_B_bonded: 3.41 restraints_weight: 0.0625 r_work: 0.2728 rms_B_bonded: 3.52 restraints_weight: 0.0312 r_work: 0.2709 rms_B_bonded: 3.67 restraints_weight: 0.0156 r_work: 0.2690 rms_B_bonded: 3.86 restraints_weight: 0.0078 r_work: 0.2669 rms_B_bonded: 4.08 restraints_weight: 0.0039 r_work: 0.2646 rms_B_bonded: 4.35 restraints_weight: 0.0020 r_work: 0.2622 rms_B_bonded: 4.68 restraints_weight: 0.0010 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 16898 Z= 0.251 Angle : 0.489 9.286 22869 Z= 0.258 Chirality : 0.045 0.143 2415 Planarity : 0.003 0.086 2968 Dihedral : 4.406 22.736 2219 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.27 (0.19), residues: 2037 helix: 1.50 (0.90), residues: 42 sheet: 0.56 (0.16), residues: 1050 loop : -0.22 (0.20), residues: 945 =============================================================================== Job complete usr+sys time: 6515.02 seconds wall clock time: 117 minutes 32.78 seconds (7052.78 seconds total)