Starting phenix.real_space_refine on Mon Mar 18 17:43:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/03_2024/6qd0_4515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/03_2024/6qd0_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_4515/03_2024/6qd0_4515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/03_2024/6qd0_4515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/03_2024/6qd0_4515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd0_4515/03_2024/6qd0_4515.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 44 5.16 5 C 6936 2.51 5 N 1820 2.21 5 O 1844 1.98 5 H 11100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.86, per 1000 atoms: 0.45 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: 18.16 Conformation dependent library (CDL) restraints added in 1.9 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: 1.75 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: 7.79 Time building geometry restraints manager: 18.73 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: 9419 15.47 - 30.93: 575 30.93 - 46.40: 186 46.40 - 61.87: 100 61.87 - 77.34: 8 Dihedral angle restraints: 10288 sinusoidal: 5604 harmonic: 4684 Sorted by residual: dihedral pdb=" CA ASN D 226 " pdb=" C ASN D 226 " pdb=" N TRP D 227 " pdb=" CA TRP D 227 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASN A 226 " pdb=" C ASN A 226 " pdb=" N TRP A 227 " pdb=" CA TRP A 227 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN B 226 " pdb=" C ASN B 226 " pdb=" N TRP B 227 " pdb=" CA TRP B 227 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 10285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 879 0.029 - 0.057: 531 0.057 - 0.086: 225 0.086 - 0.115: 105 0.115 - 0.143: 44 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA VAL A 288 " pdb=" N VAL A 288 " pdb=" C VAL A 288 " pdb=" CB VAL A 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA VAL D 288 " pdb=" N VAL D 288 " pdb=" C VAL D 288 " pdb=" CB VAL D 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL B 288 " pdb=" N VAL B 288 " pdb=" C VAL B 288 " pdb=" CB VAL B 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" N ALA A 325 " -0.040 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.010 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C LEU A 210 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 210 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 211 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LEU D 210 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU D 210 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 211 " -0.013 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.35: 8011 2.35 - 3.05: 64371 3.05 - 3.75: 74419 3.75 - 4.44: 116971 4.44 - 5.14: 176277 Nonbonded interactions: 440049 Sorted by model distance: nonbonded pdb=" H GLY C 259 " pdb=" O ALA C 313 " model vdw 1.654 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 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: 0.060 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: 0.350 Extract box with map and model: 1.670 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 71.680 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 10880 Z= 0.584 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 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 206 HIS 0.005 0.003 HIS A 323 PHE 0.026 0.003 PHE B 203 TYR 0.021 0.004 TYR D 178 ARG 0.008 0.001 ARG C 254 *********************** 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: A 95 PRO cc_start: 0.8100 (Cg_exo) cc_final: 0.7748 (Cg_endo) REVERT: A 223 PHE cc_start: 0.6441 (t80) cc_final: 0.5910 (t80) REVERT: A 243 VAL cc_start: 0.9287 (t) cc_final: 0.9048 (m) REVERT: B 95 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7805 (Cg_endo) REVERT: B 223 PHE cc_start: 0.6600 (t80) cc_final: 0.6126 (t80) REVERT: B 243 VAL cc_start: 0.9289 (t) cc_final: 0.9060 (m) REVERT: C 95 PRO cc_start: 0.8200 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: C 223 PHE cc_start: 0.6632 (t80) cc_final: 0.6133 (t80) REVERT: C 243 VAL cc_start: 0.9299 (t) cc_final: 0.9062 (m) REVERT: C 328 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8819 (tp-100) REVERT: D 33 MET cc_start: 0.5940 (mmm) cc_final: 0.5605 (mmm) REVERT: D 173 LEU cc_start: 0.8488 (tp) cc_final: 0.8269 (tp) REVERT: D 243 VAL cc_start: 0.9317 (t) cc_final: 0.9076 (m) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.5536 time to fit residues: 307.7348 Evaluate side-chains 262 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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: 6.9990 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10880 Z= 0.217 Angle : 0.698 6.547 14852 Z= 0.379 Chirality : 0.041 0.149 1784 Planarity : 0.006 0.046 1872 Dihedral : 6.660 23.812 1536 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.56 (0.21), residues: 1412 helix: -2.31 (0.16), residues: 656 sheet: -3.78 (0.56), residues: 40 loop : -2.29 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 167 HIS 0.004 0.002 HIS D 323 PHE 0.015 0.001 PHE A 223 TYR 0.014 0.002 TYR C 100 ARG 0.008 0.001 ARG B 220 *********************** 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 : 2.089 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: A 52 TYR cc_start: 0.7620 (m-10) cc_final: 0.7066 (m-10) REVERT: A 223 PHE cc_start: 0.6452 (t80) cc_final: 0.6105 (t80) REVERT: A 243 VAL cc_start: 0.9297 (t) cc_final: 0.9020 (m) REVERT: A 275 VAL cc_start: 0.8332 (t) cc_final: 0.7982 (m) REVERT: B 105 LEU cc_start: 0.8913 (mm) cc_final: 0.8688 (mm) REVERT: B 223 PHE cc_start: 0.6591 (t80) cc_final: 0.6361 (t80) REVERT: B 227 TRP cc_start: 0.8520 (t-100) cc_final: 0.8190 (t-100) REVERT: B 243 VAL cc_start: 0.9337 (t) cc_final: 0.9111 (m) REVERT: B 275 VAL cc_start: 0.8231 (t) cc_final: 0.7896 (m) REVERT: C 52 TYR cc_start: 0.7485 (m-10) cc_final: 0.6938 (m-10) REVERT: C 74 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7564 (mtpp) REVERT: C 105 LEU cc_start: 0.8800 (mm) cc_final: 0.8505 (mm) REVERT: C 117 VAL cc_start: 0.7885 (t) cc_final: 0.7620 (t) REVERT: C 223 PHE cc_start: 0.6521 (t80) cc_final: 0.6249 (t80) REVERT: C 243 VAL cc_start: 0.9278 (t) cc_final: 0.9008 (m) REVERT: C 275 VAL cc_start: 0.8217 (t) cc_final: 0.7913 (m) REVERT: D 33 MET cc_start: 0.5965 (mmm) cc_final: 0.5476 (mmp) REVERT: D 243 VAL cc_start: 0.9285 (t) cc_final: 0.9011 (m) REVERT: D 275 VAL cc_start: 0.8433 (t) cc_final: 0.8122 (m) REVERT: D 327 PHE cc_start: 0.7575 (t80) cc_final: 0.7345 (t80) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4659 time to fit residues: 210.1191 Evaluate side-chains 254 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 7.3788 ------------------------------------------------------------------------------- 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: 0.7320 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10880 Z= 0.244 Angle : 0.659 5.899 14852 Z= 0.361 Chirality : 0.040 0.141 1784 Planarity : 0.005 0.039 1872 Dihedral : 6.108 20.292 1536 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -3.05 (0.22), residues: 1412 helix: -1.51 (0.18), residues: 704 sheet: -3.48 (0.62), residues: 40 loop : -2.47 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 227 HIS 0.002 0.001 HIS A 323 PHE 0.010 0.002 PHE A 223 TYR 0.015 0.002 TYR D 100 ARG 0.006 0.001 ARG A 220 *********************** 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 319 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8879 (mm) cc_final: 0.8584 (mm) REVERT: A 243 VAL cc_start: 0.9334 (t) cc_final: 0.9123 (m) REVERT: A 275 VAL cc_start: 0.8474 (t) cc_final: 0.8153 (m) REVERT: B 52 TYR cc_start: 0.7623 (m-10) cc_final: 0.7106 (m-10) REVERT: B 105 LEU cc_start: 0.8934 (mm) cc_final: 0.8671 (mm) REVERT: B 275 VAL cc_start: 0.8217 (t) cc_final: 0.7857 (m) REVERT: C 105 LEU cc_start: 0.8866 (mm) cc_final: 0.8555 (mm) REVERT: C 106 LEU cc_start: 0.9545 (mt) cc_final: 0.9276 (pp) REVERT: C 217 GLU cc_start: 0.8079 (tp30) cc_final: 0.7745 (tp30) REVERT: C 243 VAL cc_start: 0.9308 (t) cc_final: 0.9050 (m) REVERT: C 275 VAL cc_start: 0.8462 (t) cc_final: 0.8125 (m) REVERT: D 33 MET cc_start: 0.5804 (mmm) cc_final: 0.5312 (mmm) REVERT: D 52 TYR cc_start: 0.7692 (m-10) cc_final: 0.7122 (m-10) REVERT: D 243 VAL cc_start: 0.9350 (t) cc_final: 0.9133 (m) REVERT: D 275 VAL cc_start: 0.8363 (t) cc_final: 0.8044 (m) REVERT: D 347 GLU cc_start: 0.8627 (tt0) cc_final: 0.8299 (tp30) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.4514 time to fit residues: 208.0637 Evaluate side-chains 224 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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: 10.0000 chunk 95 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 40.0000 chunk 121 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.7337 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10880 Z= 0.210 Angle : 0.606 5.361 14852 Z= 0.330 Chirality : 0.040 0.140 1784 Planarity : 0.005 0.038 1872 Dihedral : 5.718 21.561 1536 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.84 (0.22), residues: 1412 helix: -1.41 (0.18), residues: 732 sheet: -3.34 (0.66), residues: 40 loop : -2.31 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 227 HIS 0.005 0.001 HIS C 323 PHE 0.018 0.002 PHE C 341 TYR 0.013 0.002 TYR D 215 ARG 0.008 0.000 ARG B 220 *********************** 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 314 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8835 (mm) cc_final: 0.8495 (mm) REVERT: A 106 LEU cc_start: 0.9507 (mt) cc_final: 0.9256 (pp) REVERT: A 275 VAL cc_start: 0.8580 (t) cc_final: 0.8250 (m) REVERT: B 33 MET cc_start: 0.6185 (mmm) cc_final: 0.5729 (mmm) REVERT: B 105 LEU cc_start: 0.8870 (mm) cc_final: 0.8584 (mm) REVERT: B 106 LEU cc_start: 0.9531 (mt) cc_final: 0.9215 (pp) REVERT: B 140 LEU cc_start: 0.8349 (tt) cc_final: 0.8093 (tp) REVERT: B 226 ASN cc_start: 0.8719 (m-40) cc_final: 0.8486 (m-40) REVERT: B 275 VAL cc_start: 0.8325 (t) cc_final: 0.7953 (m) REVERT: C 105 LEU cc_start: 0.8870 (mm) cc_final: 0.8561 (mm) REVERT: C 170 VAL cc_start: 0.8418 (t) cc_final: 0.8191 (p) REVERT: C 243 VAL cc_start: 0.9369 (t) cc_final: 0.9165 (m) REVERT: C 275 VAL cc_start: 0.8546 (t) cc_final: 0.8234 (m) REVERT: C 327 PHE cc_start: 0.7357 (t80) cc_final: 0.7042 (t80) REVERT: C 336 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6473 (tt0) REVERT: D 33 MET cc_start: 0.5764 (mmm) cc_final: 0.5293 (mmm) REVERT: D 170 VAL cc_start: 0.8408 (t) cc_final: 0.8126 (p) REVERT: D 223 PHE cc_start: 0.6689 (t80) cc_final: 0.6408 (t80) REVERT: D 226 ASN cc_start: 0.8758 (m-40) cc_final: 0.8515 (m-40) REVERT: D 243 VAL cc_start: 0.9374 (t) cc_final: 0.9151 (m) REVERT: D 275 VAL cc_start: 0.8391 (t) cc_final: 0.8079 (m) REVERT: D 347 GLU cc_start: 0.8627 (tt0) cc_final: 0.8297 (tp30) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.4439 time to fit residues: 204.2841 Evaluate side-chains 230 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.188 Angle : 0.579 5.209 14852 Z= 0.312 Chirality : 0.040 0.135 1784 Planarity : 0.005 0.036 1872 Dihedral : 5.403 19.980 1536 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.67 (0.22), residues: 1412 helix: -1.20 (0.18), residues: 740 sheet: -3.11 (0.69), residues: 40 loop : -2.34 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 227 HIS 0.004 0.002 HIS D 323 PHE 0.014 0.001 PHE A 341 TYR 0.018 0.002 TYR D 178 ARG 0.006 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 PHE cc_start: 0.6682 (t80) cc_final: 0.6423 (t80) REVERT: A 275 VAL cc_start: 0.8647 (t) cc_final: 0.8323 (m) REVERT: A 305 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7965 (pt0) REVERT: B 105 LEU cc_start: 0.8812 (mm) cc_final: 0.8549 (mm) REVERT: B 275 VAL cc_start: 0.8394 (t) cc_final: 0.8054 (m) REVERT: C 170 VAL cc_start: 0.8406 (t) cc_final: 0.8154 (p) REVERT: C 243 VAL cc_start: 0.9378 (t) cc_final: 0.9168 (m) REVERT: C 275 VAL cc_start: 0.8523 (t) cc_final: 0.8205 (m) REVERT: C 305 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7909 (pt0) REVERT: C 327 PHE cc_start: 0.7091 (t80) cc_final: 0.6627 (t80) REVERT: D 33 MET cc_start: 0.5779 (mmm) cc_final: 0.5288 (mmm) REVERT: D 74 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7885 (mtpp) REVERT: D 105 LEU cc_start: 0.8854 (mm) cc_final: 0.8593 (mm) REVERT: D 106 LEU cc_start: 0.9474 (mt) cc_final: 0.9173 (pp) REVERT: D 223 PHE cc_start: 0.6982 (t80) cc_final: 0.6745 (t80) REVERT: D 243 VAL cc_start: 0.9377 (t) cc_final: 0.9146 (m) REVERT: D 275 VAL cc_start: 0.8551 (t) cc_final: 0.8216 (m) REVERT: D 347 GLU cc_start: 0.8630 (tt0) cc_final: 0.8301 (tp30) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.4650 time to fit residues: 201.4042 Evaluate side-chains 228 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 40.0000 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- 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 ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10880 Z= 0.198 Angle : 0.578 5.156 14852 Z= 0.310 Chirality : 0.039 0.136 1784 Planarity : 0.005 0.037 1872 Dihedral : 5.232 19.073 1536 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.63 (0.22), residues: 1412 helix: -1.12 (0.18), residues: 744 sheet: -3.11 (0.68), residues: 40 loop : -2.38 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 227 HIS 0.002 0.001 HIS A 323 PHE 0.014 0.001 PHE B 341 TYR 0.013 0.002 TYR C 178 ARG 0.006 0.000 ARG C 220 *********************** 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 285 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8812 (mm) cc_final: 0.8500 (mm) REVERT: A 223 PHE cc_start: 0.6931 (t80) cc_final: 0.6597 (t80) REVERT: A 226 ASN cc_start: 0.8695 (m-40) cc_final: 0.8457 (m-40) REVERT: A 275 VAL cc_start: 0.8622 (t) cc_final: 0.8310 (m) REVERT: A 305 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7945 (pt0) REVERT: A 327 PHE cc_start: 0.7223 (t80) cc_final: 0.6763 (t80) REVERT: B 105 LEU cc_start: 0.8806 (mm) cc_final: 0.8532 (mm) REVERT: B 226 ASN cc_start: 0.8623 (m-40) cc_final: 0.8422 (m-40) REVERT: B 275 VAL cc_start: 0.8468 (t) cc_final: 0.8126 (m) REVERT: C 105 LEU cc_start: 0.8811 (mm) cc_final: 0.8481 (mm) REVERT: C 275 VAL cc_start: 0.8603 (t) cc_final: 0.8279 (m) REVERT: C 305 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7885 (pt0) REVERT: D 33 MET cc_start: 0.5742 (mmm) cc_final: 0.5233 (mmm) REVERT: D 105 LEU cc_start: 0.8849 (mm) cc_final: 0.8592 (mm) REVERT: D 226 ASN cc_start: 0.8765 (m-40) cc_final: 0.8562 (m-40) REVERT: D 275 VAL cc_start: 0.8447 (t) cc_final: 0.8145 (m) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.4526 time to fit residues: 186.1307 Evaluate side-chains 233 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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: 0.8980 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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** D 216 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 10880 Z= 0.182 Angle : 0.554 7.817 14852 Z= 0.295 Chirality : 0.039 0.140 1784 Planarity : 0.008 0.261 1872 Dihedral : 5.074 25.722 1536 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.35 (0.22), residues: 1412 helix: -0.97 (0.18), residues: 740 sheet: -2.88 (0.71), residues: 40 loop : -2.14 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 227 HIS 0.001 0.001 HIS B 323 PHE 0.014 0.001 PHE C 341 TYR 0.008 0.001 TYR D 215 ARG 0.035 0.001 ARG A 219 *********************** 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 281 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.683 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: A 105 LEU cc_start: 0.8741 (mm) cc_final: 0.8426 (mm) REVERT: A 275 VAL cc_start: 0.8672 (t) cc_final: 0.8343 (m) REVERT: A 305 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7986 (pt0) REVERT: B 105 LEU cc_start: 0.8802 (mm) cc_final: 0.8530 (mm) REVERT: B 275 VAL cc_start: 0.8561 (t) cc_final: 0.8217 (m) REVERT: B 327 PHE cc_start: 0.7208 (t80) cc_final: 0.6990 (t80) REVERT: C 74 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7725 (mtpt) REVERT: C 105 LEU cc_start: 0.8762 (mm) cc_final: 0.8412 (mm) REVERT: C 275 VAL cc_start: 0.8652 (t) cc_final: 0.8324 (m) REVERT: C 305 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7786 (pt0) REVERT: D 33 MET cc_start: 0.5715 (mmm) cc_final: 0.5214 (mmm) REVERT: D 105 LEU cc_start: 0.8784 (mm) cc_final: 0.8540 (mm) REVERT: D 275 VAL cc_start: 0.8486 (t) cc_final: 0.8168 (m) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.4570 time to fit residues: 185.2606 Evaluate side-chains 248 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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: 1.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10880 Z= 0.149 Angle : 0.535 5.776 14852 Z= 0.282 Chirality : 0.039 0.126 1784 Planarity : 0.005 0.042 1872 Dihedral : 4.782 17.363 1536 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.19 (0.22), residues: 1412 helix: -0.69 (0.18), residues: 748 sheet: -2.52 (0.70), residues: 40 loop : -2.31 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 227 HIS 0.003 0.001 HIS B 323 PHE 0.022 0.001 PHE B 341 TYR 0.014 0.001 TYR A 215 ARG 0.014 0.000 ARG A 219 *********************** 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 290 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.694 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: A 105 LEU cc_start: 0.8747 (mm) cc_final: 0.8423 (mm) REVERT: A 275 VAL cc_start: 0.8813 (t) cc_final: 0.8491 (m) REVERT: B 105 LEU cc_start: 0.8742 (mm) cc_final: 0.8446 (mm) REVERT: B 275 VAL cc_start: 0.8681 (t) cc_final: 0.8328 (m) REVERT: B 327 PHE cc_start: 0.7163 (t80) cc_final: 0.6893 (t80) REVERT: C 74 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7673 (mtpt) REVERT: C 105 LEU cc_start: 0.8700 (mm) cc_final: 0.8355 (mm) REVERT: C 275 VAL cc_start: 0.8787 (t) cc_final: 0.8502 (m) REVERT: C 305 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7839 (pt0) REVERT: D 33 MET cc_start: 0.5867 (mmm) cc_final: 0.5362 (mmm) REVERT: D 105 LEU cc_start: 0.8732 (mm) cc_final: 0.8469 (mm) REVERT: D 275 VAL cc_start: 0.8636 (t) cc_final: 0.8306 (m) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.4546 time to fit residues: 190.1350 Evaluate side-chains 248 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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: 20.0000 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 0.4980 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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: 0.7363 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10880 Z= 0.187 Angle : 0.566 5.677 14852 Z= 0.304 Chirality : 0.039 0.135 1784 Planarity : 0.005 0.075 1872 Dihedral : 4.811 17.149 1536 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.22), residues: 1412 helix: -0.65 (0.18), residues: 756 sheet: -2.33 (0.70), residues: 40 loop : -2.28 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 227 HIS 0.003 0.001 HIS B 323 PHE 0.023 0.002 PHE C 186 TYR 0.015 0.002 TYR B 148 ARG 0.007 0.001 ARG A 219 *********************** 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 : 1.779 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: A 74 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7817 (mtpp) REVERT: A 105 LEU cc_start: 0.8774 (mm) cc_final: 0.8456 (mm) REVERT: A 275 VAL cc_start: 0.8806 (t) cc_final: 0.8445 (m) REVERT: A 305 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7904 (pt0) REVERT: B 105 LEU cc_start: 0.8780 (mm) cc_final: 0.8478 (mm) REVERT: B 226 ASN cc_start: 0.8585 (m-40) cc_final: 0.8335 (m-40) REVERT: B 275 VAL cc_start: 0.8688 (t) cc_final: 0.8360 (m) REVERT: B 327 PHE cc_start: 0.7148 (t80) cc_final: 0.6871 (t80) REVERT: C 105 LEU cc_start: 0.8768 (mm) cc_final: 0.8444 (mm) REVERT: C 226 ASN cc_start: 0.8630 (m-40) cc_final: 0.8385 (m-40) REVERT: C 275 VAL cc_start: 0.8810 (t) cc_final: 0.8483 (m) REVERT: D 33 MET cc_start: 0.5807 (mmm) cc_final: 0.5268 (mmm) REVERT: D 105 LEU cc_start: 0.8730 (mm) cc_final: 0.8455 (mm) REVERT: D 226 ASN cc_start: 0.8542 (m-40) cc_final: 0.8309 (m-40) REVERT: D 275 VAL cc_start: 0.8650 (t) cc_final: 0.8331 (m) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.4574 time to fit residues: 184.3478 Evaluate side-chains 245 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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: 20.0000 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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: 0.7356 moved from start: 0.7060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10880 Z= 0.170 Angle : 0.548 5.081 14852 Z= 0.291 Chirality : 0.039 0.130 1784 Planarity : 0.005 0.039 1872 Dihedral : 4.717 16.527 1536 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -1.92 (0.22), residues: 1412 helix: -0.49 (0.19), residues: 760 sheet: -2.09 (0.73), residues: 40 loop : -2.21 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 227 HIS 0.002 0.001 HIS B 323 PHE 0.019 0.001 PHE B 341 TYR 0.018 0.001 TYR C 148 ARG 0.007 0.000 ARG C 220 ********************** 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 283 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.804 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7810 (mtpp) REVERT: A 105 LEU cc_start: 0.8750 (mm) cc_final: 0.8430 (mm) REVERT: A 275 VAL cc_start: 0.8818 (t) cc_final: 0.8490 (m) REVERT: B 105 LEU cc_start: 0.8756 (mm) cc_final: 0.8441 (mm) REVERT: B 248 VAL cc_start: 0.8600 (t) cc_final: 0.8388 (p) REVERT: B 275 VAL cc_start: 0.8789 (t) cc_final: 0.8458 (m) REVERT: B 327 PHE cc_start: 0.7061 (t80) cc_final: 0.6845 (t80) REVERT: C 74 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7934 (mtpp) REVERT: C 105 LEU cc_start: 0.8727 (mm) cc_final: 0.8415 (mm) REVERT: C 197 MET cc_start: 0.7724 (tpp) cc_final: 0.7518 (tpp) REVERT: C 226 ASN cc_start: 0.8635 (m-40) cc_final: 0.8375 (m-40) REVERT: C 275 VAL cc_start: 0.8770 (t) cc_final: 0.8398 (m) REVERT: D 33 MET cc_start: 0.6001 (mmm) cc_final: 0.5298 (mmm) REVERT: D 105 LEU cc_start: 0.8739 (mm) cc_final: 0.8473 (mm) REVERT: D 226 ASN cc_start: 0.8667 (m-40) cc_final: 0.8407 (m-40) REVERT: D 275 VAL cc_start: 0.8653 (t) cc_final: 0.8303 (m) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.4552 time to fit residues: 186.1529 Evaluate side-chains 248 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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: 8.9990 chunk 102 optimal weight: 40.0000 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.165171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.130364 restraints weight = 73919.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135745 restraints weight = 37626.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.139317 restraints weight = 23624.290| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10880 Z= 0.229 Angle : 0.606 5.165 14852 Z= 0.329 Chirality : 0.040 0.147 1784 Planarity : 0.005 0.042 1872 Dihedral : 4.919 17.999 1536 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.22 (0.22), residues: 1412 helix: -0.74 (0.17), residues: 812 sheet: -2.41 (0.67), residues: 40 loop : -2.45 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 227 HIS 0.012 0.005 HIS C 323 PHE 0.026 0.002 PHE D 186 TYR 0.014 0.002 TYR A 215 ARG 0.008 0.001 ARG D 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4549.71 seconds wall clock time: 80 minutes 52.65 seconds (4852.65 seconds total)