Starting phenix.real_space_refine on Thu Aug 6 09:01:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbm_16545/08_2026/8cbm_16545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbm_16545/08_2026/8cbm_16545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cbm_16545/08_2026/8cbm_16545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbm_16545/08_2026/8cbm_16545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbm_16545/08_2026/8cbm_16545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbm_16545/08_2026/8cbm_16545.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 1.049 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: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 56 5.16 5 C 8934 2.51 5 N 2548 2.21 5 O 2965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14579 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3101 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 1 Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2447 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 8, 'TRANS': 286} Chain: "T" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1404 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 28, 'rna3p_pyr': 25} Link IDs: {'rna2p': 12, 'rna3p': 53} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'CDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.26 Number of scatterers: 14579 At special positions: 0 Unit cell: (103.016, 105.624, 161.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 76 15.00 O 2965 8.00 N 2548 7.00 C 8934 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: 1.24 Conformation dependent library (CDL) restraints added in 556.5 milliseconds 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3078 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 11 sheets defined 58.0% alpha, 8.4% beta 20 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.234A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 139 removed outlier: 3.625A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.387A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.638A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.729A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.012A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 139 removed outlier: 3.551A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.372A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.695A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.889A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 55 removed outlier: 4.011A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 138 removed outlier: 3.585A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 186 removed outlier: 4.356A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.630A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.584A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.641A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.614A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.655A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.359A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.672A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 85 through 97 Processing helix chain 'E' and resid 104 through 109 removed outlier: 3.906A pdb=" N LYS E 107 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.888A pdb=" N MET E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 178 Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 195 through 209 removed outlier: 4.217A pdb=" N LEU E 199 " --> pdb=" O TYR E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 231 removed outlier: 5.036A pdb=" N LYS E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 247 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 262 through 268 removed outlier: 4.556A pdb=" N TYR E 266 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 286 Processing helix chain 'E' and resid 291 through 300 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.548A pdb=" N VAL E 306 " --> pdb=" O VAL E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 332 removed outlier: 3.732A pdb=" N LYS E 331 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 353 Processing helix chain 'E' and resid 355 through 370 removed outlier: 3.865A pdb=" N THR E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 381 Processing helix chain 'E' and resid 389 through 397 removed outlier: 3.567A pdb=" N ILE E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 418 Processing helix chain 'E' and resid 423 through 431 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 125 through 168 removed outlier: 4.769A pdb=" N LYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR F 132 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 Processing helix chain 'F' and resid 182 through 202 Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 236 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 4.027A pdb=" N LYS F 268 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 282 removed outlier: 3.670A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.626A pdb=" N ALA A 13 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A 40 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 15 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 12 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 89 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 14 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.282A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.447A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE C 251 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 195 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.720A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 12 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL D 89 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 14 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 99 through 101 removed outlier: 4.127A pdb=" N ARG E 99 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE E 80 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP E 79 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 61 " --> pdb=" O LEU E 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 126 through 127 removed outlier: 3.591A pdb=" N GLU E 139 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.553A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4285 1.33 - 1.45: 2329 1.45 - 1.57: 8111 1.57 - 1.69: 149 1.69 - 1.81: 94 Bond restraints: 14968 Sorted by residual: bond pdb=" O3A CDP E 501 " pdb=" PB CDP E 501 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.580 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O3 NAD C 301 " pdb=" PA NAD C 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O3 NAD D 301 " pdb=" PA NAD D 301 " ideal model delta sigma weight residual 1.653 1.582 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 14963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 19859 1.51 - 3.03: 588 3.03 - 4.54: 122 4.54 - 6.06: 21 6.06 - 7.57: 5 Bond angle restraints: 20595 Sorted by residual: angle pdb=" C3' C T 68 " pdb=" O3' C T 68 " pdb=" P A T 69 " ideal model delta sigma weight residual 119.70 114.33 5.37 1.20e+00 6.94e-01 2.01e+01 angle pdb=" N LYS F 141 " pdb=" CA LYS F 141 " pdb=" C LYS F 141 " ideal model delta sigma weight residual 111.07 106.60 4.47 1.07e+00 8.73e-01 1.75e+01 angle pdb=" N LEU E 196 " pdb=" CA LEU E 196 " pdb=" C LEU E 196 " ideal model delta sigma weight residual 112.34 107.03 5.31 1.30e+00 5.92e-01 1.67e+01 angle pdb=" N TYR B 233 " pdb=" CA TYR B 233 " pdb=" C TYR B 233 " ideal model delta sigma weight residual 111.07 106.91 4.16 1.07e+00 8.73e-01 1.51e+01 angle pdb=" C GLY E 235 " pdb=" N GLU E 236 " pdb=" CA GLU E 236 " ideal model delta sigma weight residual 120.65 115.56 5.09 1.32e+00 5.74e-01 1.49e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 8855 33.33 - 66.66: 328 66.66 - 99.99: 29 99.99 - 133.32: 3 133.32 - 166.65: 1 Dihedral angle restraints: 9216 sinusoidal: 4413 harmonic: 4803 Sorted by residual: dihedral pdb=" O4' A T 42 " pdb=" C1' A T 42 " pdb=" N9 A T 42 " pdb=" C4 A T 42 " ideal model delta sinusoidal sigma weight residual 68.00 140.40 -72.40 1 1.70e+01 3.46e-03 2.32e+01 dihedral pdb=" C4' A T 42 " pdb=" C3' A T 42 " pdb=" O3' A T 42 " pdb=" P A T 43 " ideal model delta sinusoidal sigma weight residual -110.00 56.65 -166.65 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' U T 41 " pdb=" C3' U T 41 " pdb=" O3' U T 41 " pdb=" P A T 42 " ideal model delta sinusoidal sigma weight residual -140.00 -17.15 -122.85 1 3.50e+01 8.16e-04 1.21e+01 ... (remaining 9213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2191 0.090 - 0.179: 211 0.179 - 0.268: 7 0.268 - 0.358: 1 0.358 - 0.447: 1 Chirality restraints: 2411 Sorted by residual: chirality pdb=" P A T 69 " pdb=" OP1 A T 69 " pdb=" OP2 A T 69 " pdb=" O5' A T 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C3' CDP E 501 " pdb=" C2' CDP E 501 " pdb=" C4' CDP E 501 " pdb=" O3' CDP E 501 " both_signs ideal model delta sigma weight residual False -2.38 -2.68 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ILE E 198 " pdb=" N ILE E 198 " pdb=" C ILE E 198 " pdb=" CB ILE E 198 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2408 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.045 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.004 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 195 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C TYR E 195 " 0.040 2.00e-02 2.50e+03 pdb=" O TYR E 195 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU E 196 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.027 2.00e-02 2.50e+03 1.56e-02 4.87e+00 pdb=" C2N NAD B 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " -0.012 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " -0.011 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.024 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1647 2.74 - 3.28: 15693 3.28 - 3.82: 26770 3.82 - 4.36: 31634 4.36 - 4.90: 52134 Nonbonded interactions: 127878 Sorted by model distance: nonbonded pdb=" OG SER E 274 " pdb=" OE2 GLU E 276 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR F 291 " pdb=" OG SER F 322 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR D 153 " pdb=" OH TYR D 233 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG A 184 " pdb=" O GLY B 161 " model vdw 2.221 3.120 nonbonded pdb=" OD1 ASP C 142 " pdb=" N GLN C 146 " model vdw 2.223 3.120 ... (remaining 127873 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.005 0.153 14968 Z= 0.259 Angle : 0.610 7.569 20595 Z= 0.375 Chirality : 0.046 0.447 2411 Planarity : 0.004 0.034 2405 Dihedral : 16.574 166.654 6138 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.15 % Allowed : 0.36 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1685 helix: 2.40 (0.18), residues: 857 sheet: -0.63 (0.34), residues: 237 loop : -0.32 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG E 197 TYR 0.021 0.001 TYR F 135 PHE 0.013 0.001 PHE E 325 TRP 0.008 0.001 TRP E 415 HIS 0.003 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.26 (14968) covalent geometry : angle 0.61023 / 0.38 (20595) hydrogen bonds : bond 0.13184 / 8.24 ( 754) hydrogen bonds : angle 5.76630 / 4.13 ( 2116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9375 (tttp) cc_final: 0.9001 (ttmm) REVERT: A 81 LYS cc_start: 0.9298 (mmmm) cc_final: 0.9078 (mmmm) REVERT: A 119 ASP cc_start: 0.9151 (m-30) cc_final: 0.8850 (m-30) REVERT: C 70 ASP cc_start: 0.9068 (m-30) cc_final: 0.8814 (m-30) REVERT: C 260 GLN cc_start: 0.8164 (mt0) cc_final: 0.7955 (mm110) REVERT: D 28 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8493 (mt-10) REVERT: D 68 GLU cc_start: 0.8635 (tt0) cc_final: 0.8291 (tt0) REVERT: D 104 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8780 (mttp) REVERT: D 105 LYS cc_start: 0.9461 (mtpp) cc_final: 0.9087 (mptt) REVERT: E 89 MET cc_start: 0.8330 (mmp) cc_final: 0.7711 (mmm) REVERT: E 255 ILE cc_start: 0.9618 (mm) cc_final: 0.9268 (mm) REVERT: E 320 LYS cc_start: 0.9694 (tttt) cc_final: 0.9398 (tppt) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.1307 time to fit residues: 25.4505 Evaluate side-chains 74 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 236 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN E 94 GLN E 102 ASN E 421 GLN F 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.077420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051260 restraints weight = 52212.515| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.69 r_work: 0.2782 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14968 Z= 0.175 Angle : 0.584 7.344 20595 Z= 0.303 Chirality : 0.042 0.321 2411 Planarity : 0.005 0.051 2405 Dihedral : 16.164 167.553 3042 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.44 % Allowed : 6.05 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.21), residues: 1685 helix: 2.32 (0.18), residues: 868 sheet: -0.57 (0.33), residues: 236 loop : -0.06 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 104 TYR 0.037 0.002 TYR F 137 PHE 0.015 0.002 PHE E 325 TRP 0.015 0.001 TRP E 239 HIS 0.009 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14968) covalent geometry : angle 0.58408 / 0.30 (20595) hydrogen bonds : bond 0.04733 / 3.18 ( 754) hydrogen bonds : angle 4.94934 / 3.53 ( 2116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9187 (m-30) cc_final: 0.8930 (m-30) REVERT: C 70 ASP cc_start: 0.9086 (m-30) cc_final: 0.8858 (m-30) REVERT: D 105 LYS cc_start: 0.9507 (mtpp) cc_final: 0.9180 (mptt) REVERT: E 320 LYS cc_start: 0.9778 (tttt) cc_final: 0.9448 (tppt) REVERT: F 137 TYR cc_start: 0.8825 (t80) cc_final: 0.8601 (t80) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1083 time to fit residues: 14.6229 Evaluate side-chains 74 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 425 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 45 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.077974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051887 restraints weight = 52356.561| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.71 r_work: 0.2794 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14968 Z= 0.138 Angle : 0.518 8.649 20595 Z= 0.274 Chirality : 0.040 0.338 2411 Planarity : 0.004 0.039 2405 Dihedral : 15.821 166.429 3039 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.66 % Allowed : 7.58 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1685 helix: 2.29 (0.18), residues: 867 sheet: -0.45 (0.33), residues: 236 loop : -0.06 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 106 TYR 0.020 0.002 TYR F 135 PHE 0.013 0.001 PHE E 325 TRP 0.013 0.001 TRP E 239 HIS 0.006 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14968) covalent geometry : angle 0.51763 / 0.27 (20595) hydrogen bonds : bond 0.04159 / 2.80 ( 754) hydrogen bonds : angle 4.76638 / 3.40 ( 2116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9201 (m-30) cc_final: 0.8939 (m-30) REVERT: A 229 ASP cc_start: 0.8854 (t0) cc_final: 0.8607 (t0) REVERT: D 105 LYS cc_start: 0.9513 (mtpp) cc_final: 0.9185 (mptt) REVERT: E 89 MET cc_start: 0.7883 (mmm) cc_final: 0.7627 (mmm) REVERT: F 137 TYR cc_start: 0.8959 (t80) cc_final: 0.8758 (t80) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.0989 time to fit residues: 13.1104 Evaluate side-chains 75 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 421 GLN F 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.077089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051077 restraints weight = 52663.155| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.66 r_work: 0.2767 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14968 Z= 0.194 Angle : 0.534 8.982 20595 Z= 0.278 Chirality : 0.041 0.334 2411 Planarity : 0.004 0.038 2405 Dihedral : 15.662 167.191 3039 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.09 % Allowed : 8.60 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.21), residues: 1685 helix: 2.23 (0.18), residues: 867 sheet: -0.41 (0.33), residues: 236 loop : -0.09 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 106 TYR 0.040 0.002 TYR E 430 PHE 0.015 0.001 PHE F 312 TRP 0.009 0.001 TRP E 415 HIS 0.005 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (14968) covalent geometry : angle 0.53438 / 0.28 (20595) hydrogen bonds : bond 0.04126 / 2.78 ( 754) hydrogen bonds : angle 4.74509 / 3.39 ( 2116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9209 (m-30) cc_final: 0.8904 (m-30) REVERT: A 123 MET cc_start: 0.9052 (tmm) cc_final: 0.8816 (tmm) REVERT: A 229 ASP cc_start: 0.8871 (t0) cc_final: 0.8570 (t0) REVERT: D 105 LYS cc_start: 0.9512 (mtpp) cc_final: 0.9176 (mptt) REVERT: E 89 MET cc_start: 0.8164 (mmm) cc_final: 0.7838 (mmm) REVERT: F 137 TYR cc_start: 0.9050 (t80) cc_final: 0.8804 (t80) REVERT: F 222 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8634 (t0) outliers start: 15 outliers final: 7 residues processed: 81 average time/residue: 0.0968 time to fit residues: 12.8871 Evaluate side-chains 77 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 0.0970 chunk 21 optimal weight: 0.0770 chunk 3 optimal weight: 0.3980 chunk 134 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN C 127 ASN E 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052287 restraints weight = 52289.869| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.73 r_work: 0.2802 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14968 Z= 0.106 Angle : 0.505 10.894 20595 Z= 0.265 Chirality : 0.039 0.337 2411 Planarity : 0.004 0.039 2405 Dihedral : 15.546 166.309 3039 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.80 % Allowed : 9.26 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.21), residues: 1685 helix: 2.28 (0.18), residues: 869 sheet: -0.41 (0.33), residues: 240 loop : -0.01 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 106 TYR 0.027 0.001 TYR E 430 PHE 0.020 0.001 PHE E 278 TRP 0.012 0.001 TRP E 415 HIS 0.006 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (14968) covalent geometry : angle 0.50471 / 0.26 (20595) hydrogen bonds : bond 0.03730 / 2.54 ( 754) hydrogen bonds : angle 4.57775 / 3.26 ( 2116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9192 (m-30) cc_final: 0.8886 (m-30) REVERT: A 123 MET cc_start: 0.8986 (tmm) cc_final: 0.8776 (tmm) REVERT: D 105 LYS cc_start: 0.9511 (mtpp) cc_final: 0.9188 (mptt) REVERT: D 143 GLN cc_start: 0.8731 (mp10) cc_final: 0.8499 (pm20) REVERT: D 160 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: E 89 MET cc_start: 0.8187 (mmm) cc_final: 0.7837 (mmm) REVERT: F 137 TYR cc_start: 0.9085 (t80) cc_final: 0.8826 (t80) REVERT: F 153 LYS cc_start: 0.9014 (tppt) cc_final: 0.8671 (ptpt) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.0993 time to fit residues: 13.2942 Evaluate side-chains 81 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 128 optimal weight: 0.0070 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 111 optimal weight: 0.0060 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.078424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.052497 restraints weight = 52386.906| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.65 r_work: 0.2804 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14968 Z= 0.116 Angle : 0.498 10.608 20595 Z= 0.261 Chirality : 0.039 0.333 2411 Planarity : 0.004 0.039 2405 Dihedral : 15.430 165.367 3039 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.80 % Allowed : 10.28 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.21), residues: 1685 helix: 2.28 (0.18), residues: 870 sheet: -0.36 (0.33), residues: 236 loop : -0.08 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 106 TYR 0.024 0.001 TYR E 430 PHE 0.015 0.001 PHE E 278 TRP 0.013 0.001 TRP E 415 HIS 0.010 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14968) covalent geometry : angle 0.49765 / 0.26 (20595) hydrogen bonds : bond 0.03624 / 2.47 ( 754) hydrogen bonds : angle 4.54202 / 3.23 ( 2116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9184 (m-30) cc_final: 0.8867 (m-30) REVERT: A 123 MET cc_start: 0.8994 (tmm) cc_final: 0.8780 (tmm) REVERT: C 70 ASP cc_start: 0.9069 (m-30) cc_final: 0.8859 (m-30) REVERT: D 105 LYS cc_start: 0.9507 (mtpp) cc_final: 0.9179 (mptt) REVERT: D 143 GLN cc_start: 0.8778 (mp10) cc_final: 0.8577 (pm20) REVERT: D 160 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: E 89 MET cc_start: 0.8292 (mmm) cc_final: 0.7900 (mmm) REVERT: F 100 MET cc_start: 0.9397 (ptp) cc_final: 0.9130 (ppp) REVERT: F 137 TYR cc_start: 0.9105 (t80) cc_final: 0.8862 (t80) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.1045 time to fit residues: 14.0853 Evaluate side-chains 81 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051978 restraints weight = 52409.212| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.87 r_work: 0.2781 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14968 Z= 0.151 Angle : 0.505 9.796 20595 Z= 0.264 Chirality : 0.039 0.329 2411 Planarity : 0.004 0.039 2405 Dihedral : 15.408 165.104 3039 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.95 % Allowed : 10.57 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.21), residues: 1685 helix: 2.34 (0.18), residues: 870 sheet: -0.23 (0.34), residues: 220 loop : -0.09 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 106 TYR 0.022 0.001 TYR E 430 PHE 0.013 0.001 PHE E 278 TRP 0.013 0.001 TRP E 415 HIS 0.009 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14968) covalent geometry : angle 0.50537 / 0.26 (20595) hydrogen bonds : bond 0.03668 / 2.49 ( 754) hydrogen bonds : angle 4.53634 / 3.23 ( 2116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9183 (m-30) cc_final: 0.8839 (m-30) REVERT: A 123 MET cc_start: 0.9040 (tmm) cc_final: 0.8761 (tmm) REVERT: C 70 ASP cc_start: 0.9105 (m-30) cc_final: 0.8837 (m-30) REVERT: D 105 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9100 (mptt) REVERT: D 160 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: E 89 MET cc_start: 0.8409 (mmm) cc_final: 0.8095 (mmm) REVERT: F 137 TYR cc_start: 0.9143 (t80) cc_final: 0.8881 (t80) REVERT: F 153 LYS cc_start: 0.9004 (tppt) cc_final: 0.8638 (ptpt) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 0.1059 time to fit residues: 13.8620 Evaluate side-chains 79 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 3 optimal weight: 0.1980 chunk 159 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 40.0000 chunk 149 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051423 restraints weight = 52378.795| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.86 r_work: 0.2765 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14968 Z= 0.189 Angle : 0.542 12.784 20595 Z= 0.279 Chirality : 0.040 0.329 2411 Planarity : 0.004 0.039 2405 Dihedral : 15.434 165.831 3039 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.66 % Allowed : 10.86 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.21), residues: 1685 helix: 2.27 (0.18), residues: 870 sheet: -0.28 (0.34), residues: 220 loop : -0.11 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 106 TYR 0.023 0.001 TYR F 135 PHE 0.013 0.001 PHE F 312 TRP 0.014 0.001 TRP E 415 HIS 0.011 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (14968) covalent geometry : angle 0.54182 / 0.28 (20595) hydrogen bonds : bond 0.03817 / 2.59 ( 754) hydrogen bonds : angle 4.61542 / 3.29 ( 2116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9182 (m-30) cc_final: 0.8832 (m-30) REVERT: A 123 MET cc_start: 0.9053 (tmm) cc_final: 0.8770 (tmm) REVERT: C 70 ASP cc_start: 0.9103 (m-30) cc_final: 0.8832 (m-30) REVERT: D 160 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: E 89 MET cc_start: 0.8420 (mmm) cc_final: 0.8091 (mmm) REVERT: E 158 MET cc_start: 0.6973 (mpp) cc_final: 0.6730 (mpp) REVERT: E 391 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6506 (m90) REVERT: E 422 MET cc_start: 0.5041 (ptm) cc_final: 0.4792 (ptp) REVERT: F 137 TYR cc_start: 0.9139 (t80) cc_final: 0.8900 (t80) REVERT: F 222 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8503 (t0) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.0979 time to fit residues: 12.4890 Evaluate side-chains 76 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 391 HIS Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 162 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.078634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052194 restraints weight = 52452.849| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.87 r_work: 0.2788 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 0.037 14968 Z= 0.123 Angle : 0.519 12.302 20595 Z= 0.271 Chirality : 0.040 0.333 2411 Planarity : 0.004 0.040 2405 Dihedral : 15.390 165.960 3039 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.51 % Allowed : 11.44 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.21), residues: 1685 helix: 2.30 (0.18), residues: 870 sheet: -0.29 (0.34), residues: 220 loop : -0.09 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 106 TYR 0.023 0.001 TYR F 135 PHE 0.020 0.001 PHE F 97 TRP 0.012 0.001 TRP E 415 HIS 0.006 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14968) covalent geometry : angle 0.51914 / 0.27 (20595) hydrogen bonds : bond 0.03643 / 2.49 ( 754) hydrogen bonds : angle 4.55032 / 3.24 ( 2116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9174 (m-30) cc_final: 0.8827 (m-30) REVERT: A 123 MET cc_start: 0.9030 (tmm) cc_final: 0.8755 (tmm) REVERT: C 70 ASP cc_start: 0.9100 (m-30) cc_final: 0.8836 (m-30) REVERT: D 160 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: E 89 MET cc_start: 0.8426 (mmm) cc_final: 0.8080 (mmm) REVERT: E 391 HIS cc_start: 0.6876 (OUTLIER) cc_final: 0.6538 (m90) REVERT: E 422 MET cc_start: 0.4878 (ptm) cc_final: 0.4643 (ptp) REVERT: F 137 TYR cc_start: 0.9139 (t80) cc_final: 0.8905 (t80) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.1006 time to fit residues: 12.7922 Evaluate side-chains 77 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 391 HIS Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 135 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.079296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052854 restraints weight = 52103.007| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.88 r_work: 0.2810 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14968 Z= 0.112 Angle : 0.507 11.757 20595 Z= 0.267 Chirality : 0.039 0.334 2411 Planarity : 0.004 0.040 2405 Dihedral : 15.262 165.739 3039 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.58 % Allowed : 11.66 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.21), residues: 1685 helix: 2.33 (0.18), residues: 870 sheet: -0.22 (0.34), residues: 220 loop : -0.05 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 106 TYR 0.021 0.001 TYR F 135 PHE 0.012 0.001 PHE F 97 TRP 0.014 0.001 TRP E 415 HIS 0.005 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (14968) covalent geometry : angle 0.50680 / 0.27 (20595) hydrogen bonds : bond 0.03448 / 2.37 ( 754) hydrogen bonds : angle 4.47483 / 3.18 ( 2116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9148 (m-30) cc_final: 0.8788 (m-30) REVERT: A 123 MET cc_start: 0.9014 (tmm) cc_final: 0.8744 (tmm) REVERT: C 70 ASP cc_start: 0.9104 (m-30) cc_final: 0.8840 (m-30) REVERT: D 105 LYS cc_start: 0.9535 (mtpp) cc_final: 0.9050 (mptt) REVERT: D 160 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: E 89 MET cc_start: 0.8404 (mmm) cc_final: 0.8052 (mmm) REVERT: E 158 MET cc_start: 0.6981 (mpp) cc_final: 0.6765 (mpp) REVERT: E 422 MET cc_start: 0.4871 (ptm) cc_final: 0.4657 (ptp) REVERT: F 137 TYR cc_start: 0.9168 (t80) cc_final: 0.8902 (t80) outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 0.1011 time to fit residues: 12.8986 Evaluate side-chains 76 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 333 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 16 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.079366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052904 restraints weight = 52104.438| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.91 r_work: 0.2810 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14968 Z= 0.113 Angle : 0.506 11.487 20595 Z= 0.266 Chirality : 0.039 0.334 2411 Planarity : 0.004 0.040 2405 Dihedral : 15.197 165.786 3039 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.36 % Allowed : 12.03 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.21), residues: 1685 helix: 2.34 (0.18), residues: 874 sheet: -0.18 (0.34), residues: 220 loop : -0.04 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 106 TYR 0.023 0.001 TYR F 135 PHE 0.010 0.001 PHE E 278 TRP 0.014 0.001 TRP E 415 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14968) covalent geometry : angle 0.50622 / 0.27 (20595) hydrogen bonds : bond 0.03409 / 2.33 ( 754) hydrogen bonds : angle 4.43975 / 3.16 ( 2116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.32 seconds wall clock time: 61 minutes 48.81 seconds (3708.81 seconds total)