Starting phenix.real_space_refine on Fri Jun 13 10:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0a_36758/06_2025/8k0a_36758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0a_36758/06_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_36758/06_2025/8k0a_36758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0a_36758/06_2025/8k0a_36758.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0a_36758/06_2025/8k0a_36758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0a_36758/06_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-5710/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: 12.24, per 1000 atoms: 0.82 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: 3.20 Conformation dependent library (CDL) restraints added in 1.8 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: 2.04 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: 5.44 Time building geometry restraints manager: 3.87 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: 0.10 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: 20.360 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: 0.770 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.050 ------------------------------------------------------------------------------- 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 : 1.701 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3602 time to fit residues: 105.6096 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 : 1.663 ------------------------------------------------------------------------------- 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 = 0.067486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.053207 restraints weight = 41703.212| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.80 r_work: 0.2559 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 4.80472 ( 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 : 1.500 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8164 (mt-10) REVERT: D 148 ASN cc_start: 0.8777 (m-40) cc_final: 0.8574 (m-40) REVERT: E 205 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.3109 time to fit residues: 65.0820 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 : 1.617 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.068094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.053900 restraints weight = 41245.223| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.76 r_work: 0.2582 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15330 Z= 0.129 Angle : 0.481 4.956 20799 Z= 0.259 Chirality : 0.042 0.132 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.833 50.153 2049 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.21 % Allowed : 7.25 % Favored : 91.54 % 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: 1.93 (0.23), residues: 588 sheet: 0.44 (0.26), residues: 381 loop : -0.77 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 194 HIS 0.003 0.001 HIS C 108 PHE 0.010 0.001 PHE A 216 TYR 0.014 0.001 TYR C 107 ARG 0.004 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 648) hydrogen bonds : angle 4.54541 ( 1818) covalent geometry : bond 0.00298 (15330) covalent geometry : angle 0.48106 (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 147 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.630 Fit side-chains REVERT: A 243 ARG cc_start: 0.7377 (mmt180) cc_final: 0.7093 (mmp-170) REVERT: B 57 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8697 (mtmm) REVERT: C 210 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.7612 (t70) REVERT: C 243 ARG cc_start: 0.7361 (mmt180) cc_final: 0.7064 (mmp-170) REVERT: E 243 ARG cc_start: 0.7425 (mmt180) cc_final: 0.7115 (mmp-170) outliers start: 19 outliers final: 11 residues processed: 147 average time/residue: 0.3107 time to fit residues: 65.7717 Evaluate side-chains 124 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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: 1.9990 chunk 168 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.053909 restraints weight = 41417.256| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.75 r_work: 0.2575 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2138 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= 0.135 Angle : 0.472 5.386 20799 Z= 0.253 Chirality : 0.042 0.131 2169 Planarity : 0.003 0.034 2736 Dihedral : 4.725 50.032 2049 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.40 % Allowed : 8.40 % Favored : 90.20 % 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: 0.70 (0.21), residues: 1827 helix: 2.11 (0.23), residues: 591 sheet: 0.51 (0.27), residues: 363 loop : -0.72 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 428 HIS 0.003 0.001 HIS A 108 PHE 0.009 0.001 PHE F 138 TYR 0.014 0.001 TYR A 107 ARG 0.003 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 648) hydrogen bonds : angle 4.49179 ( 1818) covalent geometry : bond 0.00314 (15330) covalent geometry : angle 0.47235 (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 143 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.550 Fit side-chains REVERT: A 243 ARG cc_start: 0.7391 (mmt180) cc_final: 0.7106 (mmp-170) REVERT: A 312 THR cc_start: 0.9563 (p) cc_final: 0.9068 (t) REVERT: B 57 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8669 (mtmm) REVERT: C 210 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.7639 (t70) REVERT: C 243 ARG cc_start: 0.7378 (mmt180) cc_final: 0.7066 (mmp-170) REVERT: C 312 THR cc_start: 0.9562 (p) cc_final: 0.9069 (t) REVERT: E 243 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7104 (mmp-170) REVERT: E 312 THR cc_start: 0.9556 (p) cc_final: 0.9077 (t) outliers start: 22 outliers final: 14 residues processed: 143 average time/residue: 0.2849 time to fit residues: 59.4254 Evaluate side-chains 127 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 73 GLN 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 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: 2.9990 chunk 166 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 400 GLN D 73 GLN E 400 GLN F 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.050843 restraints weight = 42360.740| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.79 r_work: 0.2512 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2257 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= 0.265 Angle : 0.560 6.539 20799 Z= 0.299 Chirality : 0.044 0.145 2169 Planarity : 0.004 0.035 2736 Dihedral : 5.015 49.673 2049 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.97 % Allowed : 9.35 % Favored : 88.68 % 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: 0.60 (0.21), residues: 1827 helix: 1.92 (0.24), residues: 606 sheet: 0.53 (0.28), residues: 363 loop : -0.78 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 428 HIS 0.005 0.001 HIS A 108 PHE 0.014 0.001 PHE F 138 TYR 0.021 0.001 TYR A 107 ARG 0.003 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 648) hydrogen bonds : angle 4.77588 ( 1818) covalent geometry : bond 0.00618 (15330) covalent geometry : angle 0.56023 (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 141 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.802 Fit side-chains REVERT: A 243 ARG cc_start: 0.7437 (mmt180) cc_final: 0.7127 (mmp-170) REVERT: A 369 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: C 210 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.7750 (t0) REVERT: C 243 ARG cc_start: 0.7449 (mmt180) cc_final: 0.7112 (mmp-170) REVERT: D 73 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (mm-40) REVERT: E 243 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7140 (mmp-170) outliers start: 31 outliers final: 18 residues processed: 138 average time/residue: 0.3427 time to fit residues: 67.3635 Evaluate side-chains 129 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 40 ILE 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 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 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 40 ILE 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: 0.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 C 254 GLN E 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.052832 restraints weight = 41515.167| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.80 r_work: 0.2563 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15330 Z= 0.121 Angle : 0.474 7.585 20799 Z= 0.250 Chirality : 0.042 0.142 2169 Planarity : 0.003 0.036 2736 Dihedral : 4.697 49.689 2049 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.40 % Allowed : 10.62 % Favored : 87.98 % 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: 0.90 (0.21), residues: 1827 helix: 2.25 (0.23), residues: 591 sheet: 0.63 (0.28), residues: 363 loop : -0.58 (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 C 108 PHE 0.008 0.001 PHE D 138 TYR 0.014 0.001 TYR D 119 ARG 0.003 0.000 ARG F 76 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 648) hydrogen bonds : angle 4.52804 ( 1818) covalent geometry : bond 0.00279 (15330) covalent geometry : angle 0.47377 (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 144 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.585 Fit side-chains REVERT: A 243 ARG cc_start: 0.7435 (mmt180) cc_final: 0.7124 (mmp-170) REVERT: A 312 THR cc_start: 0.9609 (p) cc_final: 0.9130 (t) REVERT: B 126 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7450 (pttm) REVERT: C 210 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.7660 (t70) REVERT: C 243 ARG cc_start: 0.7401 (mmt180) cc_final: 0.7078 (mmp-170) REVERT: C 312 THR cc_start: 0.9589 (p) cc_final: 0.9087 (t) REVERT: C 368 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8231 (mt-10) REVERT: C 369 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: D 73 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8464 (mm-40) REVERT: D 126 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7393 (pttm) REVERT: E 243 ARG cc_start: 0.7441 (mmt180) cc_final: 0.7136 (mmp-170) REVERT: E 312 THR cc_start: 0.9588 (p) cc_final: 0.9114 (t) REVERT: F 126 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7391 (pttm) outliers start: 22 outliers final: 14 residues processed: 140 average time/residue: 0.2920 time to fit residues: 59.2414 Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 100 SER 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 C residue 369 GLN 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 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: 0.6980 chunk 93 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** F 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 = 0.3066 r_free = 0.3066 target = 0.067729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.053571 restraints weight = 41443.910| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.78 r_work: 0.2581 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15330 Z= 0.103 Angle : 0.459 6.489 20799 Z= 0.242 Chirality : 0.041 0.134 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.517 48.449 2049 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.34 % Allowed : 11.58 % Favored : 87.09 % 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: 2.34 (0.23), residues: 588 sheet: 0.69 (0.28), residues: 363 loop : -0.53 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 428 HIS 0.002 0.001 HIS F 97 PHE 0.007 0.001 PHE F 138 TYR 0.009 0.001 TYR E 107 ARG 0.003 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 648) hydrogen bonds : angle 4.39764 ( 1818) covalent geometry : bond 0.00237 (15330) covalent geometry : angle 0.45919 (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 157 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7463 (mmt180) cc_final: 0.7153 (mmp-170) REVERT: A 312 THR cc_start: 0.9570 (p) cc_final: 0.9036 (t) REVERT: B 126 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7577 (pttm) REVERT: C 210 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.7621 (t70) REVERT: C 243 ARG cc_start: 0.7439 (mmt180) cc_final: 0.7113 (mmp-170) REVERT: C 312 THR cc_start: 0.9553 (p) cc_final: 0.9011 (t) REVERT: C 369 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: D 73 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8391 (mm-40) REVERT: D 126 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7543 (pttm) REVERT: E 243 ARG cc_start: 0.7485 (mmt180) cc_final: 0.7173 (mmp-170) REVERT: E 312 THR cc_start: 0.9556 (p) cc_final: 0.9027 (t) REVERT: F 126 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7564 (pttm) outliers start: 21 outliers final: 15 residues processed: 153 average time/residue: 0.3321 time to fit residues: 74.4802 Evaluate side-chains 141 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 381 LEU Chi-restraints excluded: chain B residue 100 SER 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 C residue 369 GLN 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 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 359 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 152 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 100 optimal weight: 0.0040 chunk 156 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 D 49 ASN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.054537 restraints weight = 41081.104| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.71 r_work: 0.2610 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2637 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= 0.095 Angle : 0.456 6.954 20799 Z= 0.240 Chirality : 0.041 0.132 2169 Planarity : 0.003 0.046 2736 Dihedral : 4.406 47.610 2049 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.46 % Allowed : 12.60 % Favored : 85.94 % 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: 1.06 (0.21), residues: 1827 helix: 2.42 (0.23), residues: 588 sheet: 0.70 (0.27), residues: 363 loop : -0.49 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 194 HIS 0.002 0.001 HIS D 97 PHE 0.007 0.001 PHE F 138 TYR 0.008 0.001 TYR E 107 ARG 0.003 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 648) hydrogen bonds : angle 4.31603 ( 1818) covalent geometry : bond 0.00219 (15330) covalent geometry : angle 0.45636 (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 154 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7500 (mmt180) cc_final: 0.7183 (mmp-170) REVERT: A 369 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6633 (mt0) REVERT: C 210 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7912 (t70) REVERT: C 243 ARG cc_start: 0.7478 (mmt180) cc_final: 0.7156 (mmp-170) REVERT: C 369 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6611 (mt0) REVERT: D 73 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8396 (mm-40) REVERT: E 210 ASP cc_start: 0.8519 (m-30) cc_final: 0.7701 (t0) REVERT: E 243 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7198 (mmp-170) REVERT: F 57 LYS cc_start: 0.9158 (ptpp) cc_final: 0.8857 (mtmm) REVERT: F 139 ASP cc_start: 0.7952 (m-30) cc_final: 0.7626 (m-30) outliers start: 23 outliers final: 16 residues processed: 152 average time/residue: 0.2949 time to fit residues: 64.7738 Evaluate side-chains 132 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 73 GLN 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 359 ARG Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 100 SER 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: 0.9980 chunk 42 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 0.0570 chunk 29 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3092 r_free = 0.3092 target = 0.068826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054709 restraints weight = 40830.526| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.78 r_work: 0.2609 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2695 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= 0.099 Angle : 0.465 9.120 20799 Z= 0.243 Chirality : 0.041 0.183 2169 Planarity : 0.003 0.034 2736 Dihedral : 4.351 46.058 2049 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.40 % Allowed : 12.98 % Favored : 85.62 % 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: 1.08 (0.21), residues: 1827 helix: 2.46 (0.23), residues: 588 sheet: 0.80 (0.29), residues: 333 loop : -0.50 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 194 HIS 0.002 0.001 HIS F 97 PHE 0.007 0.001 PHE A 338 TYR 0.010 0.001 TYR C 212 ARG 0.008 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 648) hydrogen bonds : angle 4.30734 ( 1818) covalent geometry : bond 0.00229 (15330) covalent geometry : angle 0.46506 (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 144 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7516 (mmt180) cc_final: 0.7208 (mmp-170) REVERT: A 368 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8074 (mt-10) REVERT: A 369 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6629 (mt0) REVERT: C 210 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7869 (t70) REVERT: C 243 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7167 (mmp-170) REVERT: C 369 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6590 (mt0) REVERT: E 210 ASP cc_start: 0.8458 (m-30) cc_final: 0.8013 (t70) REVERT: E 243 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7196 (mmp-170) outliers start: 22 outliers final: 16 residues processed: 142 average time/residue: 0.3291 time to fit residues: 66.6825 Evaluate side-chains 132 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 381 LEU 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 359 ARG Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 100 SER 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: 4.9990 chunk 78 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 164 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3071 r_free = 0.3071 target = 0.067841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.053709 restraints weight = 41421.667| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.78 r_work: 0.2585 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15330 Z= 0.145 Angle : 0.488 8.958 20799 Z= 0.257 Chirality : 0.042 0.182 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.432 45.722 2049 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.15 % Allowed : 13.23 % Favored : 85.62 % 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: 1.10 (0.21), residues: 1827 helix: 2.43 (0.23), residues: 591 sheet: 0.81 (0.29), residues: 330 loop : -0.45 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 194 HIS 0.002 0.001 HIS A 108 PHE 0.009 0.001 PHE F 138 TYR 0.011 0.001 TYR E 107 ARG 0.005 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 648) hydrogen bonds : angle 4.37050 ( 1818) covalent geometry : bond 0.00339 (15330) covalent geometry : angle 0.48796 (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 133 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.887 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7530 (mmt180) cc_final: 0.7214 (mmp-170) REVERT: A 369 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6689 (mt0) REVERT: C 210 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7900 (t70) REVERT: C 243 ARG cc_start: 0.7494 (mmt180) cc_final: 0.7164 (mmp-170) REVERT: E 210 ASP cc_start: 0.8505 (m-30) cc_final: 0.7660 (t0) REVERT: E 243 ARG cc_start: 0.7523 (mmt180) cc_final: 0.7214 (mmp-170) REVERT: F 139 ASP cc_start: 0.7956 (m-30) cc_final: 0.7753 (m-30) outliers start: 18 outliers final: 16 residues processed: 131 average time/residue: 0.3197 time to fit residues: 61.0313 Evaluate side-chains 131 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 381 LEU 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 359 ARG Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 100 SER 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: 0.0980 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 374 ASN D 49 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.051387 restraints weight = 42135.974| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.71 r_work: 0.2524 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15330 Z= 0.271 Angle : 0.582 9.165 20799 Z= 0.309 Chirality : 0.045 0.180 2169 Planarity : 0.004 0.065 2736 Dihedral : 4.890 46.909 2049 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.34 % Allowed : 13.10 % Favored : 85.56 % 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: 2.05 (0.23), residues: 609 sheet: 0.59 (0.28), residues: 354 loop : -0.48 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 315 HIS 0.004 0.001 HIS A 108 PHE 0.015 0.001 PHE F 138 TYR 0.019 0.001 TYR E 107 ARG 0.005 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 648) hydrogen bonds : angle 4.72023 ( 1818) covalent geometry : bond 0.00630 (15330) covalent geometry : angle 0.58229 (20799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6678.66 seconds wall clock time: 116 minutes 45.42 seconds (7005.42 seconds total)