Starting phenix.real_space_refine on Fri May 16 21:38:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0a_36758/05_2025/8k0a_36758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0a_36758/05_2025/8k0a_36758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0a_36758/05_2025/8k0a_36758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0a_36758/05_2025/8k0a_36758.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0a_36758/05_2025/8k0a_36758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0a_36758/05_2025/8k0a_36758.cif" } resolution = 3.12 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 9435 2.51 5 N 2655 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14952 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 1 Chain: "B" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1453 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Restraints were copied for chains: C, E, D, F Time building chain proxies: 11.32, per 1000 atoms: 0.76 Number of scatterers: 14952 At special positions: 0 Unit cell: (118.575, 112.625, 93.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2799 8.00 N 2655 7.00 C 9435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 2.0 seconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 37.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 8 through 11 removed outlier: 3.617A pdb=" N GLN A 11 " --> pdb=" O ASN A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 8 through 11' Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 169 through 179 removed outlier: 4.011A pdb=" N TYR A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.635A pdb=" N ALA A 204 " --> pdb=" O TRP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.211A pdb=" N THR A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 4.861A pdb=" N ALA A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.632A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.917A pdb=" N ASP A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 436 through 452 removed outlier: 3.814A pdb=" N MET A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.597A pdb=" N LEU B 36 " --> pdb=" O TRP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.707A pdb=" N GLU B 90 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 11 removed outlier: 3.617A pdb=" N GLN C 11 " --> pdb=" O ASN C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 8 through 11' Processing helix chain 'C' and resid 22 through 26 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 169 through 179 removed outlier: 4.010A pdb=" N TYR C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY C 176 " --> pdb=" O TRP C 172 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.635A pdb=" N ALA C 204 " --> pdb=" O TRP C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.211A pdb=" N THR C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 4.861A pdb=" N ALA C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 346 through 362 removed outlier: 3.632A pdb=" N GLY C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.918A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 433 Processing helix chain 'C' and resid 436 through 452 removed outlier: 3.813A pdb=" N MET C 452 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.597A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.707A pdb=" N GLU D 90 " --> pdb=" O TRP D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 11 removed outlier: 3.617A pdb=" N GLN E 11 " --> pdb=" O ASN E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 11' Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 27 through 38 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 162 through 168 Processing helix chain 'E' and resid 169 through 179 removed outlier: 4.010A pdb=" N TYR E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY E 176 " --> pdb=" O TRP E 172 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 210 removed outlier: 3.635A pdb=" N ALA E 204 " --> pdb=" O TRP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 244 through 249 removed outlier: 4.211A pdb=" N THR E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 removed outlier: 4.861A pdb=" N ALA E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 346 through 362 removed outlier: 3.631A pdb=" N GLY E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 382 removed outlier: 3.918A pdb=" N ASP E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 433 Processing helix chain 'E' and resid 436 through 452 removed outlier: 3.814A pdb=" N MET E 452 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.597A pdb=" N LEU F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 58 Processing helix chain 'F' and resid 70 through 83 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.707A pdb=" N GLU F 90 " --> pdb=" O TRP F 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.695A pdb=" N VAL A 20 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.780A pdb=" N ILE A 152 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 144 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 82 removed outlier: 3.590A pdb=" N ASP A 66 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A 57 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 98 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 removed outlier: 3.532A pdb=" N ASP A 120 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY A 113 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 118 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.693A pdb=" N THR A 321 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.454A pdb=" N MET B 44 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 68 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR B 42 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 43 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 158 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG B 45 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS B 140 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG B 154 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE B 138 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE B 156 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR B 136 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 158 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL B 134 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 114 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 104 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B 116 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 102 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.695A pdb=" N VAL C 20 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.779A pdb=" N ILE C 152 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 144 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.591A pdb=" N ASP C 66 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 57 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 98 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.534A pdb=" N ASP C 120 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 113 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 118 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AB4, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.693A pdb=" N THR C 321 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.455A pdb=" N MET D 44 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN D 68 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR D 42 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR D 43 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU D 158 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG D 45 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS D 140 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG D 154 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE D 138 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE D 156 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR D 136 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU D 158 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL D 134 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA D 114 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 104 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG D 116 " --> pdb=" O CYS D 102 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS D 102 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.694A pdb=" N VAL E 20 " --> pdb=" O LEU E 392 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 48 removed outlier: 6.779A pdb=" N ILE E 152 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS E 144 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 78 through 82 removed outlier: 3.590A pdb=" N ASP E 66 " --> pdb=" O MET E 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP E 57 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 98 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 102 through 104 removed outlier: 3.534A pdb=" N ASP E 120 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY E 113 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 118 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 187 removed outlier: 3.693A pdb=" N THR E 321 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.455A pdb=" N MET F 44 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN F 68 " --> pdb=" O TYR F 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR F 42 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR F 43 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU F 158 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG F 45 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS F 140 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG F 154 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE F 138 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE F 156 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR F 136 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU F 158 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL F 134 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 114 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE F 104 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG F 116 " --> pdb=" O CYS F 102 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS F 102 " --> pdb=" O ARG F 116 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1818 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: 4.87 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5052 1.34 - 1.46: 3483 1.46 - 1.58: 6702 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 15330 Sorted by residual: bond pdb=" C THR C 3 " pdb=" O THR C 3 " ideal model delta sigma weight residual 1.246 1.233 0.013 9.20e-03 1.18e+04 1.96e+00 bond pdb=" C THR E 3 " pdb=" O THR E 3 " ideal model delta sigma weight residual 1.246 1.234 0.012 9.20e-03 1.18e+04 1.81e+00 bond pdb=" C THR A 3 " pdb=" O THR A 3 " ideal model delta sigma weight residual 1.246 1.234 0.012 9.20e-03 1.18e+04 1.65e+00 bond pdb=" N GLY A 64 " pdb=" CA GLY A 64 " ideal model delta sigma weight residual 1.460 1.448 0.012 1.26e-02 6.30e+03 9.66e-01 bond pdb=" N GLY E 64 " pdb=" CA GLY E 64 " ideal model delta sigma weight residual 1.460 1.448 0.012 1.26e-02 6.30e+03 9.49e-01 ... (remaining 15325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 19280 1.05 - 2.11: 1221 2.11 - 3.16: 218 3.16 - 4.22: 59 4.22 - 5.27: 21 Bond angle restraints: 20799 Sorted by residual: angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 112.12 109.88 2.24 8.40e-01 1.42e+00 7.12e+00 angle pdb=" N ILE B 66 " pdb=" CA ILE B 66 " pdb=" C ILE B 66 " ideal model delta sigma weight residual 112.12 109.88 2.24 8.40e-01 1.42e+00 7.10e+00 angle pdb=" N ILE F 66 " pdb=" CA ILE F 66 " pdb=" C ILE F 66 " ideal model delta sigma weight residual 112.12 109.89 2.23 8.40e-01 1.42e+00 7.02e+00 angle pdb=" N THR E 312 " pdb=" CA THR E 312 " pdb=" C THR E 312 " ideal model delta sigma weight residual 111.56 114.92 -3.36 1.38e+00 5.25e-01 5.92e+00 angle pdb=" N THR C 312 " pdb=" CA THR C 312 " pdb=" C THR C 312 " ideal model delta sigma weight residual 111.56 114.90 -3.34 1.38e+00 5.25e-01 5.87e+00 ... (remaining 20794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 8106 17.53 - 35.07: 688 35.07 - 52.60: 149 52.60 - 70.13: 36 70.13 - 87.67: 42 Dihedral angle restraints: 9021 sinusoidal: 3687 harmonic: 5334 Sorted by residual: dihedral pdb=" CA ASP E 210 " pdb=" C ASP E 210 " pdb=" N GLN E 211 " pdb=" CA GLN E 211 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP C 210 " pdb=" C ASP C 210 " pdb=" N GLN C 211 " pdb=" CA GLN C 211 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A 210 " pdb=" C ASP A 210 " pdb=" N GLN A 211 " pdb=" CA GLN A 211 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1234 0.030 - 0.059: 565 0.059 - 0.089: 222 0.089 - 0.118: 107 0.118 - 0.148: 41 Chirality restraints: 2169 Sorted by residual: chirality pdb=" CA VAL C 191 " pdb=" N VAL C 191 " pdb=" C VAL C 191 " pdb=" CB VAL C 191 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA VAL E 191 " pdb=" N VAL E 191 " pdb=" C VAL E 191 " pdb=" CB VAL E 191 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2166 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 310 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO E 311 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 310 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A 311 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 310 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 311 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 311 " -0.028 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 823 2.73 - 3.27: 13982 3.27 - 3.82: 23450 3.82 - 4.36: 29490 4.36 - 4.90: 52743 Nonbonded interactions: 120488 Sorted by model distance: nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 282 " model vdw 2.189 3.040 nonbonded pdb=" OD2 ASP C 238 " pdb=" OG SER C 282 " model vdw 2.190 3.040 nonbonded pdb=" OD2 ASP E 238 " pdb=" OG SER E 282 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR E 241 " pdb=" O ALA E 272 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A 241 " pdb=" O ALA A 272 " model vdw 2.192 3.040 ... (remaining 120483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.140 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: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.090 Set scattering table: 0.360 Process input model: 37.940 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.003 0.031 15330 Z= 0.144 Angle : 0.609 5.273 20799 Z= 0.365 Chirality : 0.045 0.148 2169 Planarity : 0.004 0.053 2736 Dihedral : 15.541 87.666 5589 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1827 helix: 0.64 (0.23), residues: 597 sheet: 0.62 (0.27), residues: 366 loop : -1.49 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 428 HIS 0.005 0.001 HIS A 108 PHE 0.012 0.001 PHE C 310 TYR 0.028 0.001 TYR E 107 ARG 0.006 0.001 ARG F 76 Details of bonding type rmsd hydrogen bonds : bond 0.14118 ( 648) hydrogen bonds : angle 5.86345 ( 1818) covalent geometry : bond 0.00298 (15330) covalent geometry : angle 0.60870 (20799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.666 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3489 time to fit residues: 101.7380 Evaluate side-chains 121 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 211 GLN B 73 GLN C 73 GLN C 211 GLN D 73 GLN E 73 GLN E 211 GLN F 73 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.053127 restraints weight = 41706.628| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.84 r_work: 0.2557 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15330 Z= 0.172 Angle : 0.529 5.141 20799 Z= 0.287 Chirality : 0.043 0.134 2169 Planarity : 0.004 0.038 2736 Dihedral : 5.028 47.510 2049 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.95 % Allowed : 6.17 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1827 helix: 1.39 (0.23), residues: 606 sheet: 0.36 (0.26), residues: 381 loop : -1.02 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 428 HIS 0.004 0.001 HIS A 108 PHE 0.018 0.001 PHE A 216 TYR 0.021 0.001 TYR E 107 ARG 0.005 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 648) hydrogen bonds : angle 4.80474 ( 1818) covalent geometry : bond 0.00396 (15330) covalent geometry : angle 0.52946 (20799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8163 (mt-10) REVERT: D 148 ASN cc_start: 0.8774 (m-40) cc_final: 0.8571 (m-40) REVERT: E 205 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8480 (tm-30) outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.3039 time to fit residues: 63.8833 Evaluate side-chains 123 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 73 GLN C 213 HIS D 73 GLN E 213 HIS F 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.054145 restraints weight = 41190.367| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.76 r_work: 0.2588 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15330 Z= 0.120 Angle : 0.477 4.950 20799 Z= 0.256 Chirality : 0.042 0.133 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.814 50.131 2049 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.21 % Allowed : 7.32 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1827 helix: 1.89 (0.23), residues: 591 sheet: 0.45 (0.27), residues: 381 loop : -0.75 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 194 HIS 0.003 0.001 HIS E 108 PHE 0.009 0.001 PHE A 216 TYR 0.014 0.001 TYR C 107 ARG 0.003 0.000 ARG E 164 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 648) hydrogen bonds : angle 4.53271 ( 1818) covalent geometry : bond 0.00277 (15330) covalent geometry : angle 0.47708 (20799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.792 Fit side-chains REVERT: A 243 ARG cc_start: 0.7367 (mmt180) cc_final: 0.6982 (mmp-170) REVERT: B 57 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8701 (mtmm) REVERT: C 210 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.7597 (t70) REVERT: C 243 ARG cc_start: 0.7344 (mmt180) cc_final: 0.6935 (mmp-170) REVERT: E 243 ARG cc_start: 0.7413 (mmt180) cc_final: 0.6993 (mmp-170) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 0.3035 time to fit residues: 65.2607 Evaluate side-chains 125 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 1 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN F 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.055265 restraints weight = 41118.862| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.73 r_work: 0.2620 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15330 Z= 0.092 Angle : 0.447 5.388 20799 Z= 0.238 Chirality : 0.041 0.129 2169 Planarity : 0.003 0.034 2736 Dihedral : 4.562 49.740 2049 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.34 % Allowed : 8.08 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1827 helix: 2.10 (0.23), residues: 591 sheet: 0.54 (0.27), residues: 381 loop : -0.57 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 194 HIS 0.002 0.000 HIS C 108 PHE 0.007 0.001 PHE A 216 TYR 0.009 0.001 TYR E 107 ARG 0.003 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 648) hydrogen bonds : angle 4.41076 ( 1818) covalent geometry : bond 0.00207 (15330) covalent geometry : angle 0.44719 (20799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.558 Fit side-chains REVERT: A 243 ARG cc_start: 0.7394 (mmt180) cc_final: 0.7112 (mmp-170) REVERT: A 312 THR cc_start: 0.9530 (p) cc_final: 0.9029 (t) REVERT: B 57 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8653 (mtmm) REVERT: C 210 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.7565 (t70) REVERT: C 243 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7057 (mmp-170) REVERT: C 312 THR cc_start: 0.9534 (p) cc_final: 0.9039 (t) REVERT: E 90 MET cc_start: 0.9150 (tpt) cc_final: 0.8914 (tpt) REVERT: E 210 ASP cc_start: 0.8508 (m-30) cc_final: 0.7619 (t0) REVERT: E 243 ARG cc_start: 0.7411 (mmt180) cc_final: 0.7126 (mmp-170) REVERT: E 312 THR cc_start: 0.9526 (p) cc_final: 0.9036 (t) outliers start: 21 outliers final: 13 residues processed: 149 average time/residue: 0.2852 time to fit residues: 61.5434 Evaluate side-chains 129 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 71 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 99 optimal weight: 0.0060 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN D 49 ASN D 73 GLN E 400 GLN F 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.050544 restraints weight = 42619.990| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.74 r_work: 0.2504 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 15330 Z= 0.332 Angle : 0.606 6.798 20799 Z= 0.322 Chirality : 0.045 0.146 2169 Planarity : 0.004 0.035 2736 Dihedral : 5.095 49.921 2049 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.78 % Allowed : 9.41 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1827 helix: 1.88 (0.23), residues: 606 sheet: 0.46 (0.28), residues: 357 loop : -0.79 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 428 HIS 0.005 0.001 HIS A 108 PHE 0.016 0.002 PHE F 138 TYR 0.023 0.001 TYR A 107 ARG 0.004 0.000 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 648) hydrogen bonds : angle 4.86119 ( 1818) covalent geometry : bond 0.00773 (15330) covalent geometry : angle 0.60564 (20799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.638 Fit side-chains REVERT: A 243 ARG cc_start: 0.7459 (mmt180) cc_final: 0.7144 (mmp-170) REVERT: C 210 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.7815 (t0) REVERT: C 243 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7128 (mmp-170) REVERT: E 243 ARG cc_start: 0.7482 (mmt180) cc_final: 0.7144 (mmp-170) outliers start: 28 outliers final: 19 residues processed: 133 average time/residue: 0.3229 time to fit residues: 60.8272 Evaluate side-chains 124 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 138 optimal weight: 0.0770 chunk 182 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN E 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.052529 restraints weight = 41594.349| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.79 r_work: 0.2561 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15330 Z= 0.132 Angle : 0.484 7.681 20799 Z= 0.256 Chirality : 0.042 0.132 2169 Planarity : 0.003 0.036 2736 Dihedral : 4.757 50.033 2049 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 10.18 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1827 helix: 2.24 (0.23), residues: 591 sheet: 0.57 (0.28), residues: 363 loop : -0.59 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 428 HIS 0.003 0.001 HIS A 108 PHE 0.008 0.001 PHE D 138 TYR 0.012 0.001 TYR E 107 ARG 0.003 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 648) hydrogen bonds : angle 4.56566 ( 1818) covalent geometry : bond 0.00306 (15330) covalent geometry : angle 0.48415 (20799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.975 Fit side-chains REVERT: A 243 ARG cc_start: 0.7432 (mmt180) cc_final: 0.7122 (mmp-170) REVERT: A 312 THR cc_start: 0.9621 (p) cc_final: 0.9154 (t) REVERT: A 369 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6803 (mt0) REVERT: B 126 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7456 (pttm) REVERT: C 210 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.7707 (t70) REVERT: C 243 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7078 (mmp-170) REVERT: C 312 THR cc_start: 0.9606 (p) cc_final: 0.9127 (t) REVERT: D 73 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8240 (mm-40) REVERT: D 126 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7370 (pttm) REVERT: E 243 ARG cc_start: 0.7437 (mmt180) cc_final: 0.7131 (mmp-170) REVERT: E 312 THR cc_start: 0.9603 (p) cc_final: 0.9140 (t) REVERT: F 126 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7428 (pttm) outliers start: 27 outliers final: 17 residues processed: 143 average time/residue: 0.2967 time to fit residues: 62.5386 Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 145 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 67 optimal weight: 0.0050 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.055470 restraints weight = 41085.043| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.74 r_work: 0.2631 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15330 Z= 0.081 Angle : 0.447 6.776 20799 Z= 0.234 Chirality : 0.041 0.132 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.371 47.529 2049 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.21 % Allowed : 11.20 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1827 helix: 2.42 (0.23), residues: 588 sheet: 0.71 (0.29), residues: 333 loop : -0.56 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 428 HIS 0.002 0.001 HIS E 48 PHE 0.007 0.001 PHE B 138 TYR 0.008 0.001 TYR F 119 ARG 0.003 0.000 ARG F 76 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 648) hydrogen bonds : angle 4.29345 ( 1818) covalent geometry : bond 0.00181 (15330) covalent geometry : angle 0.44664 (20799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.276 Fit side-chains REVERT: A 243 ARG cc_start: 0.7485 (mmt180) cc_final: 0.7253 (mmp80) REVERT: A 312 THR cc_start: 0.9521 (p) cc_final: 0.8976 (t) REVERT: C 210 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7917 (t70) REVERT: C 243 ARG cc_start: 0.7468 (mmt180) cc_final: 0.7159 (mmp-170) REVERT: C 312 THR cc_start: 0.9516 (p) cc_final: 0.8962 (t) REVERT: D 73 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8162 (mm-40) REVERT: E 90 MET cc_start: 0.9157 (tpt) cc_final: 0.8914 (tpt) REVERT: E 210 ASP cc_start: 0.8415 (m-30) cc_final: 0.7632 (t0) REVERT: E 243 ARG cc_start: 0.7476 (mmt180) cc_final: 0.7174 (mmp-170) REVERT: E 312 THR cc_start: 0.9506 (p) cc_final: 0.8971 (t) REVERT: F 75 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8657 (tm-30) REVERT: F 139 ASP cc_start: 0.7974 (m-30) cc_final: 0.7653 (m-30) outliers start: 19 outliers final: 14 residues processed: 168 average time/residue: 0.3155 time to fit residues: 76.3722 Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 152 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN F 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.054658 restraints weight = 41018.479| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.82 r_work: 0.2617 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15330 Z= 0.105 Angle : 0.471 8.973 20799 Z= 0.245 Chirality : 0.042 0.176 2169 Planarity : 0.003 0.064 2736 Dihedral : 4.370 47.006 2049 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.15 % Allowed : 12.28 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.05 (0.21), residues: 1827 helix: 2.49 (0.23), residues: 588 sheet: 0.70 (0.29), residues: 333 loop : -0.52 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 194 HIS 0.002 0.001 HIS A 108 PHE 0.007 0.001 PHE F 138 TYR 0.009 0.001 TYR C 212 ARG 0.004 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 648) hydrogen bonds : angle 4.30742 ( 1818) covalent geometry : bond 0.00244 (15330) covalent geometry : angle 0.47141 (20799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7521 (mmt180) cc_final: 0.7294 (mmp80) REVERT: A 369 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6477 (mt0) REVERT: C 210 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7934 (t70) REVERT: C 243 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7168 (mmp-170) REVERT: E 210 ASP cc_start: 0.8486 (m-30) cc_final: 0.7648 (t0) REVERT: E 243 ARG cc_start: 0.7501 (mmt180) cc_final: 0.7200 (mmp-170) outliers start: 18 outliers final: 13 residues processed: 148 average time/residue: 0.3434 time to fit residues: 71.0115 Evaluate side-chains 133 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 99 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN D 73 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.051972 restraints weight = 41572.044| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.68 r_work: 0.2545 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15330 Z= 0.235 Angle : 0.545 8.858 20799 Z= 0.287 Chirality : 0.044 0.174 2169 Planarity : 0.003 0.036 2736 Dihedral : 4.684 46.899 2049 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.40 % Allowed : 12.21 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1827 helix: 2.20 (0.23), residues: 609 sheet: 0.58 (0.28), residues: 357 loop : -0.48 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 315 HIS 0.004 0.001 HIS A 108 PHE 0.013 0.001 PHE F 138 TYR 0.016 0.001 TYR C 107 ARG 0.009 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 648) hydrogen bonds : angle 4.56469 ( 1818) covalent geometry : bond 0.00550 (15330) covalent geometry : angle 0.54517 (20799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.595 Fit side-chains REVERT: A 243 ARG cc_start: 0.7553 (mmt180) cc_final: 0.6233 (mtp85) REVERT: A 369 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6715 (mt0) REVERT: C 210 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.7650 (t70) REVERT: C 243 ARG cc_start: 0.7522 (mmt180) cc_final: 0.7181 (mmp-170) REVERT: C 368 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7431 (mt-10) REVERT: E 243 ARG cc_start: 0.7542 (mmt180) cc_final: 0.7219 (mmp-170) outliers start: 22 outliers final: 20 residues processed: 128 average time/residue: 0.3181 time to fit residues: 57.8212 Evaluate side-chains 126 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 13 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 164 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.054586 restraints weight = 41426.680| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.74 r_work: 0.2613 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15330 Z= 0.092 Angle : 0.476 8.033 20799 Z= 0.249 Chirality : 0.042 0.161 2169 Planarity : 0.003 0.034 2736 Dihedral : 4.440 46.040 2049 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.02 % Allowed : 12.60 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.16 (0.21), residues: 1827 helix: 2.74 (0.23), residues: 567 sheet: 0.72 (0.28), residues: 333 loop : -0.47 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 194 HIS 0.002 0.001 HIS E 48 PHE 0.007 0.001 PHE C 361 TYR 0.016 0.001 TYR D 119 ARG 0.009 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 648) hydrogen bonds : angle 4.33968 ( 1818) covalent geometry : bond 0.00209 (15330) covalent geometry : angle 0.47609 (20799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.643 Fit side-chains REVERT: A 243 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7235 (mmp-170) REVERT: B 126 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7364 (pttm) REVERT: C 210 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7867 (t70) REVERT: C 243 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7175 (mmp-170) REVERT: C 368 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7301 (mt-10) REVERT: D 73 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8353 (mm-40) REVERT: E 210 ASP cc_start: 0.8508 (m-30) cc_final: 0.7668 (t0) REVERT: E 243 ARG cc_start: 0.7492 (mmt180) cc_final: 0.7184 (mmp-170) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.3382 time to fit residues: 66.6592 Evaluate side-chains 135 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 181 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 0.0060 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.053287 restraints weight = 41544.197| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.74 r_work: 0.2587 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15330 Z= 0.132 Angle : 0.489 8.191 20799 Z= 0.256 Chirality : 0.042 0.157 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.448 44.948 2049 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.15 % Allowed : 12.66 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.22 (0.21), residues: 1827 helix: 2.76 (0.23), residues: 570 sheet: 0.77 (0.29), residues: 330 loop : -0.43 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 194 HIS 0.002 0.001 HIS C 108 PHE 0.009 0.001 PHE E 338 TYR 0.011 0.001 TYR C 107 ARG 0.010 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 648) hydrogen bonds : angle 4.36823 ( 1818) covalent geometry : bond 0.00309 (15330) covalent geometry : angle 0.48895 (20799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6370.71 seconds wall clock time: 112 minutes 40.69 seconds (6760.69 seconds total)