Starting phenix.real_space_refine on Sun Sep 13 11:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ach_9592/09_2026/6ach_9592.map" } resolution = 3.2 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= 0.000 sd= 0.016 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 16 5.49 5 S 136 5.16 5 C 14536 2.51 5 N 4136 2.21 5 O 4416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23240 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 4.05, per 1000 atoms: 0.17 Number of scatterers: 23240 At special positions: 0 Unit cell: (126.896, 126.896, 119.504, 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 136 16.00 P 16 15.00 O 4416 8.00 N 4136 7.00 C 14536 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: 1.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 48.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.254A pdb=" N PHE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.771A pdb=" N GLY A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 4.253A pdb=" N PHE B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.770A pdb=" N GLY B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 300 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR C 10 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 removed outlier: 4.254A pdb=" N PHE C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.770A pdb=" N GLY C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 300 Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 312 through 328 Processing helix chain 'C' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR D 10 " --> pdb=" O TYR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 4.253A pdb=" N PHE D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.589A pdb=" N LEU D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.770A pdb=" N GLY D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 300 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 312 through 328 Processing helix chain 'D' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 4.254A pdb=" N PHE E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 266 through 277 removed outlier: 3.771A pdb=" N GLY E 270 " --> pdb=" O GLU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 297 through 300 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 312 through 328 Processing helix chain 'E' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA F 54 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 4.254A pdb=" N PHE F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 247 through 251 Processing helix chain 'F' and resid 266 through 277 removed outlier: 3.770A pdb=" N GLY F 270 " --> pdb=" O GLU F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 297 through 300 Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 312 through 328 Processing helix chain 'F' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR G 10 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 4.254A pdb=" N PHE G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 166 Processing helix chain 'G' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 217 Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'G' and resid 266 through 277 removed outlier: 3.771A pdb=" N GLY G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE G 286 " --> pdb=" O PRO G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 297 through 300 Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 312 through 328 Processing helix chain 'G' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP G 336 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG G 350 " --> pdb=" O MET G 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 11 removed outlier: 3.864A pdb=" N TYR H 10 " --> pdb=" O TYR H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 72 removed outlier: 4.061A pdb=" N ALA H 54 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 removed outlier: 4.254A pdb=" N PHE H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 166 Processing helix chain 'H' and resid 184 through 196 removed outlier: 3.588A pdb=" N LEU H 188 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 217 Processing helix chain 'H' and resid 247 through 251 Processing helix chain 'H' and resid 266 through 277 removed outlier: 3.770A pdb=" N GLY H 270 " --> pdb=" O GLU H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 297 through 300 Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 312 through 328 Processing helix chain 'H' and resid 330 through 350 removed outlier: 3.970A pdb=" N ASP H 336 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG H 350 " --> pdb=" O MET H 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114 removed outlier: 5.940A pdb=" N LEU A 40 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR A 81 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY A 42 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 83 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG A 44 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY A 78 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS A 26 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS B 26 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 78 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU B 40 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR B 81 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 42 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 83 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL A 175 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA A 235 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 177 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL B 175 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA B 235 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 177 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 110 through 114 removed outlier: 5.940A pdb=" N LEU C 40 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR C 81 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY C 42 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 83 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 44 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY C 78 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS C 26 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS D 26 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY D 78 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU D 40 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR D 81 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY D 42 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE D 83 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG D 44 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL C 175 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA C 235 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 177 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL D 175 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA D 235 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA D 177 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 114 removed outlier: 5.940A pdb=" N LEU E 40 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR E 81 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY E 42 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE E 83 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG E 44 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY E 78 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS E 26 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS F 26 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY F 78 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU F 40 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR F 81 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY F 42 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE F 83 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG F 44 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL E 175 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA E 235 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA E 177 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL F 175 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA F 235 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA F 177 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 110 through 114 removed outlier: 5.940A pdb=" N LEU G 40 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR G 81 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY G 42 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE G 83 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG G 44 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY G 78 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS G 26 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS H 26 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY H 78 " --> pdb=" O HIS H 32 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU H 40 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR H 81 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY H 42 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE H 83 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG H 44 " --> pdb=" O ILE H 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL G 175 " --> pdb=" O ILE G 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA G 235 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA G 177 " --> pdb=" O ALA G 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 198 through 202 removed outlier: 6.752A pdb=" N VAL H 175 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA H 235 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA H 177 " --> pdb=" O ALA H 235 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3256 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: 3.63 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4008 1.31 - 1.43: 6056 1.43 - 1.56: 13336 1.56 - 1.69: 48 1.69 - 1.81: 240 Bond restraints: 23688 Sorted by residual: bond pdb=" C3B NAD G 400 " pdb=" C4B NAD G 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD C 400 " pdb=" C4B NAD C 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD H 400 " pdb=" C4B NAD H 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD A 400 " pdb=" C4B NAD A 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD F 400 " pdb=" C4B NAD F 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 23683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 31193 3.37 - 6.74: 655 6.74 - 10.11: 104 10.11 - 13.48: 48 13.48 - 16.85: 24 Bond angle restraints: 32024 Sorted by residual: angle pdb=" N1A NAD C 400 " pdb=" C6A NAD C 400 " pdb=" N6A NAD C 400 " ideal model delta sigma weight residual 119.35 102.50 16.85 3.00e+00 1.11e-01 3.16e+01 angle pdb=" N1A NAD D 400 " pdb=" C6A NAD D 400 " pdb=" N6A NAD D 400 " ideal model delta sigma weight residual 119.35 102.52 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" N1A NAD E 400 " pdb=" C6A NAD E 400 " pdb=" N6A NAD E 400 " ideal model delta sigma weight residual 119.35 102.54 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" N1A NAD H 400 " pdb=" C6A NAD H 400 " pdb=" N6A NAD H 400 " ideal model delta sigma weight residual 119.35 102.54 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" N1A NAD F 400 " pdb=" C6A NAD F 400 " pdb=" N6A NAD F 400 " ideal model delta sigma weight residual 119.35 102.54 16.81 3.00e+00 1.11e-01 3.14e+01 ... (remaining 32019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.73: 12792 11.73 - 23.45: 1030 23.45 - 35.18: 250 35.18 - 46.90: 80 46.90 - 58.63: 72 Dihedral angle restraints: 14224 sinusoidal: 5776 harmonic: 8448 Sorted by residual: dihedral pdb=" CA ILE E 136 " pdb=" C ILE E 136 " pdb=" N SER E 137 " pdb=" CA SER E 137 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE H 136 " pdb=" C ILE H 136 " pdb=" N SER H 137 " pdb=" CA SER H 137 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE B 136 " pdb=" C ILE B 136 " pdb=" N SER B 137 " pdb=" CA SER B 137 " ideal model delta harmonic sigma weight residual 180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 14221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2280 0.064 - 0.128: 964 0.128 - 0.191: 188 0.191 - 0.255: 0 0.255 - 0.319: 16 Chirality restraints: 3448 Sorted by residual: chirality pdb=" C3B NAD B 400 " pdb=" C2B NAD B 400 " pdb=" C4B NAD B 400 " pdb=" O3B NAD B 400 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3B NAD D 400 " pdb=" C2B NAD D 400 " pdb=" C4B NAD D 400 " pdb=" O3B NAD D 400 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3D NAD D 400 " pdb=" C2D NAD D 400 " pdb=" C4D NAD D 400 " pdb=" O3D NAD D 400 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3445 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 37 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO F 38 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 38 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 38 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 37 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO D 38 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 38 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 38 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 37 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 38 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.031 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5725 2.79 - 3.32: 20148 3.32 - 3.84: 37426 3.84 - 4.37: 44949 4.37 - 4.90: 79882 Nonbonded interactions: 188130 Sorted by model distance: nonbonded pdb=" OG1 THR H 43 " pdb=" OG1 THR H 112 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR A 43 " pdb=" OG1 THR A 112 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR C 43 " pdb=" OG1 THR C 112 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B 43 " pdb=" OG1 THR B 112 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR F 43 " pdb=" OG1 THR F 112 " model vdw 2.261 3.040 ... (remaining 188125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.080 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.016 0.230 23688 Z= 0.695 Angle : 1.356 16.851 32024 Z= 0.662 Chirality : 0.071 0.319 3448 Planarity : 0.007 0.056 4200 Dihedral : 10.690 58.630 8880 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.03 % Allowed : 4.11 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.92 (0.12), residues: 2912 helix: -2.54 (0.10), residues: 1368 sheet: -1.72 (0.19), residues: 504 loop : -2.85 (0.15), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG E 190 TYR 0.035 0.005 TYR B 186 PHE 0.031 0.006 PHE C 102 TRP 0.017 0.004 TRP G 46 HIS 0.012 0.003 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.01550 / 0.69 (23688) covalent geometry : angle 1.35630 / 0.66 (32024) hydrogen bonds : bond 0.14455 / 9.36 ( 1128) hydrogen bonds : angle 6.29663 / 4.47 ( 3256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.852 Fit side-chains REVERT: A 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt) REVERT: B 346 MET cc_start: 0.7944 (mmm) cc_final: 0.7740 (mmt) REVERT: C 346 MET cc_start: 0.7941 (mmm) cc_final: 0.7737 (mmt) REVERT: D 346 MET cc_start: 0.7945 (mmm) cc_final: 0.7740 (mmt) REVERT: E 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7737 (mmt) REVERT: F 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt) REVERT: G 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt) REVERT: H 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7736 (mmt) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.1755 time to fit residues: 157.5558 Evaluate side-chains 384 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 179 GLN A 193 HIS A 293 ASN A 302 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 179 GLN B 193 HIS B 293 ASN B 302 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 179 GLN C 193 HIS C 293 ASN C 302 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN D 179 GLN D 193 HIS D 293 ASN D 302 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 179 GLN E 193 HIS E 293 ASN E 302 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 ASN F 179 GLN F 193 HIS F 293 ASN F 302 ASN ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 179 GLN G 193 HIS G 293 ASN G 302 ASN ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN H 179 GLN H 193 HIS H 293 ASN H 302 ASN ** H 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.177069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106265 restraints weight = 106501.014| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.89 r_work: 0.2857 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23688 Z= 0.122 Angle : 0.616 6.625 32024 Z= 0.324 Chirality : 0.044 0.141 3448 Planarity : 0.004 0.040 4200 Dihedral : 6.033 37.951 3352 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.74 % Allowed : 10.70 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.14), residues: 2912 helix: -0.76 (0.13), residues: 1416 sheet: -1.02 (0.21), residues: 512 loop : -2.19 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 347 TYR 0.011 0.001 TYR F 6 PHE 0.013 0.002 PHE A 99 TRP 0.008 0.002 TRP G 46 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23688) covalent geometry : angle 0.61555 / 0.32 (32024) hydrogen bonds : bond 0.04208 / 2.74 ( 1128) hydrogen bonds : angle 4.82338 / 3.41 ( 3256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 408 time to evaluate : 0.919 Fit side-chains REVERT: A 219 LYS cc_start: 0.7378 (mttt) cc_final: 0.7137 (mttp) REVERT: A 346 MET cc_start: 0.8832 (mmm) cc_final: 0.8600 (mmm) REVERT: A 363 ARG cc_start: 0.8007 (tmt170) cc_final: 0.7731 (tmt170) REVERT: B 219 LYS cc_start: 0.7390 (mttt) cc_final: 0.7153 (mttp) REVERT: B 346 MET cc_start: 0.8844 (mmm) cc_final: 0.8614 (mmm) REVERT: B 363 ARG cc_start: 0.8010 (tmt170) cc_final: 0.7735 (tmt170) REVERT: C 219 LYS cc_start: 0.7384 (mttt) cc_final: 0.7147 (mttp) REVERT: C 346 MET cc_start: 0.8836 (mmm) cc_final: 0.8607 (mmm) REVERT: C 363 ARG cc_start: 0.8009 (tmt170) cc_final: 0.7733 (tmt170) REVERT: D 219 LYS cc_start: 0.7404 (mttt) cc_final: 0.7168 (mttp) REVERT: D 346 MET cc_start: 0.8845 (mmm) cc_final: 0.8612 (mmm) REVERT: D 363 ARG cc_start: 0.7997 (tmt170) cc_final: 0.7722 (tmt170) REVERT: E 219 LYS cc_start: 0.7394 (mttt) cc_final: 0.7156 (mttp) REVERT: E 346 MET cc_start: 0.8843 (mmm) cc_final: 0.8612 (mmm) REVERT: E 363 ARG cc_start: 0.8012 (tmt170) cc_final: 0.7736 (tmt170) REVERT: F 219 LYS cc_start: 0.7406 (mttt) cc_final: 0.7171 (mttp) REVERT: F 346 MET cc_start: 0.8848 (mmm) cc_final: 0.8614 (mmm) REVERT: F 363 ARG cc_start: 0.8005 (tmt170) cc_final: 0.7729 (tmt170) REVERT: G 219 LYS cc_start: 0.7378 (mttt) cc_final: 0.7142 (mttp) REVERT: G 346 MET cc_start: 0.8841 (mmm) cc_final: 0.8609 (mmm) REVERT: G 363 ARG cc_start: 0.8005 (tmt170) cc_final: 0.7731 (tmt170) REVERT: H 219 LYS cc_start: 0.7405 (mttt) cc_final: 0.7170 (mttp) REVERT: H 346 MET cc_start: 0.8853 (mmm) cc_final: 0.8622 (mmm) REVERT: H 363 ARG cc_start: 0.8007 (tmt170) cc_final: 0.7730 (tmt170) outliers start: 40 outliers final: 32 residues processed: 432 average time/residue: 0.1725 time to fit residues: 116.1343 Evaluate side-chains 393 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 361 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 22 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 107 ASN A 193 HIS A 359 HIS B 32 HIS B 107 ASN B 193 HIS B 359 HIS C 32 HIS C 107 ASN C 193 HIS C 359 HIS D 32 HIS D 107 ASN D 193 HIS D 359 HIS E 32 HIS E 107 ASN E 193 HIS E 359 HIS F 32 HIS F 107 ASN F 193 HIS F 359 HIS G 32 HIS G 107 ASN G 193 HIS G 359 HIS H 32 HIS H 107 ASN H 193 HIS H 359 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.172603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100752 restraints weight = 104356.047| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.71 r_work: 0.2768 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 23688 Z= 0.238 Angle : 0.655 6.854 32024 Z= 0.338 Chirality : 0.047 0.147 3448 Planarity : 0.004 0.033 4200 Dihedral : 5.682 39.234 3352 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.77 % Allowed : 11.73 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.15), residues: 2912 helix: -0.05 (0.13), residues: 1424 sheet: -1.06 (0.21), residues: 496 loop : -1.89 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 364 TYR 0.011 0.002 TYR F 152 PHE 0.011 0.002 PHE B 99 TRP 0.011 0.002 TRP B 46 HIS 0.004 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (23688) covalent geometry : angle 0.65473 / 0.34 (32024) hydrogen bonds : bond 0.04988 / 3.23 ( 1128) hydrogen bonds : angle 4.62133 / 3.27 ( 3256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 392 time to evaluate : 0.911 Fit side-chains REVERT: A 46 TRP cc_start: 0.8351 (t-100) cc_final: 0.7747 (t-100) REVERT: A 219 LYS cc_start: 0.7352 (mttt) cc_final: 0.6991 (mttp) REVERT: A 363 ARG cc_start: 0.8099 (tmt170) cc_final: 0.7895 (tmt170) REVERT: B 46 TRP cc_start: 0.8347 (t-100) cc_final: 0.7743 (t-100) REVERT: B 219 LYS cc_start: 0.7364 (mttt) cc_final: 0.7006 (mttp) REVERT: B 363 ARG cc_start: 0.8108 (tmt170) cc_final: 0.7906 (tmt170) REVERT: C 46 TRP cc_start: 0.8343 (t-100) cc_final: 0.7739 (t-100) REVERT: C 219 LYS cc_start: 0.7353 (mttt) cc_final: 0.6994 (mttp) REVERT: C 363 ARG cc_start: 0.8095 (tmt170) cc_final: 0.7894 (tmt170) REVERT: D 46 TRP cc_start: 0.8355 (t-100) cc_final: 0.7751 (t-100) REVERT: D 219 LYS cc_start: 0.7349 (mttt) cc_final: 0.6987 (mttp) REVERT: D 363 ARG cc_start: 0.8106 (tmt170) cc_final: 0.7904 (tmt170) REVERT: E 46 TRP cc_start: 0.8343 (t-100) cc_final: 0.7740 (t-100) REVERT: E 219 LYS cc_start: 0.7366 (mttt) cc_final: 0.7009 (mttp) REVERT: E 363 ARG cc_start: 0.8091 (tmt170) cc_final: 0.7888 (tmt170) REVERT: F 46 TRP cc_start: 0.8354 (t-100) cc_final: 0.7752 (t-100) REVERT: F 219 LYS cc_start: 0.7366 (mttt) cc_final: 0.7011 (mttp) REVERT: G 46 TRP cc_start: 0.8350 (t-100) cc_final: 0.7747 (t-100) REVERT: G 219 LYS cc_start: 0.7359 (mttt) cc_final: 0.7001 (mttp) REVERT: G 363 ARG cc_start: 0.8098 (tmt170) cc_final: 0.7896 (tmt170) REVERT: H 46 TRP cc_start: 0.8348 (t-100) cc_final: 0.7746 (t-100) REVERT: H 219 LYS cc_start: 0.7359 (mttt) cc_final: 0.6998 (mttp) REVERT: H 363 ARG cc_start: 0.8102 (tmt170) cc_final: 0.7899 (tmt170) outliers start: 64 outliers final: 56 residues processed: 432 average time/residue: 0.1603 time to fit residues: 110.4995 Evaluate side-chains 432 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 9 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 179 GLN E 179 GLN F 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.172968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101097 restraints weight = 107344.498| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.97 r_work: 0.2771 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 23688 Z= 0.208 Angle : 0.624 6.298 32024 Z= 0.324 Chirality : 0.046 0.149 3448 Planarity : 0.003 0.030 4200 Dihedral : 5.553 37.915 3352 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.62 % Allowed : 12.24 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.15), residues: 2912 helix: 0.34 (0.13), residues: 1424 sheet: -0.94 (0.21), residues: 496 loop : -1.64 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 364 TYR 0.010 0.002 TYR F 284 PHE 0.012 0.002 PHE H 99 TRP 0.009 0.002 TRP E 46 HIS 0.004 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (23688) covalent geometry : angle 0.62450 / 0.32 (32024) hydrogen bonds : bond 0.04456 / 2.89 ( 1128) hydrogen bonds : angle 4.46814 / 3.16 ( 3256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 384 time to evaluate : 0.834 Fit side-chains REVERT: A 16 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8813 (tp) REVERT: A 46 TRP cc_start: 0.8285 (t-100) cc_final: 0.7742 (t-100) REVERT: A 183 ASN cc_start: 0.7405 (t0) cc_final: 0.7175 (t0) REVERT: A 219 LYS cc_start: 0.7336 (mttt) cc_final: 0.6950 (mttp) REVERT: B 16 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8807 (tp) REVERT: B 46 TRP cc_start: 0.8289 (t-100) cc_final: 0.7742 (t-100) REVERT: B 183 ASN cc_start: 0.7390 (t0) cc_final: 0.7161 (t0) REVERT: B 219 LYS cc_start: 0.7331 (mttt) cc_final: 0.6943 (mttp) REVERT: C 16 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8804 (tp) REVERT: C 46 TRP cc_start: 0.8281 (t-100) cc_final: 0.7733 (t-100) REVERT: C 183 ASN cc_start: 0.7390 (t0) cc_final: 0.7160 (t0) REVERT: C 219 LYS cc_start: 0.7328 (mttt) cc_final: 0.6940 (mttp) REVERT: D 16 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8803 (tp) REVERT: D 46 TRP cc_start: 0.8302 (t-100) cc_final: 0.7758 (t-100) REVERT: D 183 ASN cc_start: 0.7391 (t0) cc_final: 0.7165 (t0) REVERT: D 219 LYS cc_start: 0.7330 (mttt) cc_final: 0.6942 (mttp) REVERT: E 16 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8806 (tp) REVERT: E 46 TRP cc_start: 0.8276 (t-100) cc_final: 0.7732 (t-100) REVERT: E 183 ASN cc_start: 0.7395 (t0) cc_final: 0.7167 (t0) REVERT: E 219 LYS cc_start: 0.7334 (mttt) cc_final: 0.6946 (mttp) REVERT: F 16 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8807 (tp) REVERT: F 46 TRP cc_start: 0.8300 (t-100) cc_final: 0.7757 (t-100) REVERT: F 183 ASN cc_start: 0.7395 (t0) cc_final: 0.7168 (t0) REVERT: F 219 LYS cc_start: 0.7329 (mttt) cc_final: 0.6941 (mttp) REVERT: G 16 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8809 (tp) REVERT: G 46 TRP cc_start: 0.8283 (t-100) cc_final: 0.7738 (t-100) REVERT: G 183 ASN cc_start: 0.7396 (t0) cc_final: 0.7167 (t0) REVERT: G 219 LYS cc_start: 0.7331 (mttt) cc_final: 0.6944 (mttp) REVERT: H 16 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8810 (tp) REVERT: H 46 TRP cc_start: 0.8289 (t-100) cc_final: 0.7741 (t-100) REVERT: H 183 ASN cc_start: 0.7397 (t0) cc_final: 0.7167 (t0) REVERT: H 219 LYS cc_start: 0.7336 (mttt) cc_final: 0.6946 (mttp) outliers start: 84 outliers final: 56 residues processed: 432 average time/residue: 0.1596 time to fit residues: 109.1054 Evaluate side-chains 440 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 376 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 240 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.173398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129976 restraints weight = 119647.173| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 8.03 r_work: 0.2619 rms_B_bonded: 6.49 restraints_weight: 2.0000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23688 Z= 0.201 Angle : 0.604 6.176 32024 Z= 0.313 Chirality : 0.045 0.149 3448 Planarity : 0.003 0.028 4200 Dihedral : 5.369 37.198 3352 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.79 % Allowed : 12.41 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.15), residues: 2912 helix: 0.60 (0.13), residues: 1424 sheet: -0.70 (0.22), residues: 496 loop : -1.48 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 347 TYR 0.009 0.002 TYR B 284 PHE 0.011 0.002 PHE H 99 TRP 0.007 0.001 TRP H 46 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (23688) covalent geometry : angle 0.60404 / 0.31 (32024) hydrogen bonds : bond 0.04343 / 2.82 ( 1128) hydrogen bonds : angle 4.38054 / 3.10 ( 3256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 355 time to evaluate : 0.787 Fit side-chains REVERT: A 16 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8902 (tp) REVERT: A 46 TRP cc_start: 0.8440 (t-100) cc_final: 0.7869 (t-100) REVERT: A 219 LYS cc_start: 0.7170 (mttt) cc_final: 0.6764 (mttp) REVERT: B 16 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8910 (tp) REVERT: B 46 TRP cc_start: 0.8440 (t-100) cc_final: 0.7857 (t-100) REVERT: B 219 LYS cc_start: 0.7180 (mttt) cc_final: 0.6774 (mttp) REVERT: C 16 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8907 (tp) REVERT: C 46 TRP cc_start: 0.8430 (t-100) cc_final: 0.7847 (t-100) REVERT: C 219 LYS cc_start: 0.7175 (mttt) cc_final: 0.6765 (mttp) REVERT: D 16 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8904 (tp) REVERT: D 46 TRP cc_start: 0.8440 (t-100) cc_final: 0.7856 (t-100) REVERT: D 219 LYS cc_start: 0.7177 (mttt) cc_final: 0.6769 (mttp) REVERT: E 16 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8908 (tp) REVERT: E 46 TRP cc_start: 0.8427 (t-100) cc_final: 0.7850 (t-100) REVERT: E 219 LYS cc_start: 0.7170 (mttt) cc_final: 0.6762 (mttp) REVERT: F 16 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8908 (tp) REVERT: F 46 TRP cc_start: 0.8443 (t-100) cc_final: 0.7868 (t-100) REVERT: F 219 LYS cc_start: 0.7179 (mttt) cc_final: 0.6777 (mttp) REVERT: G 16 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8912 (tp) REVERT: G 46 TRP cc_start: 0.8426 (t-100) cc_final: 0.7849 (t-100) REVERT: G 219 LYS cc_start: 0.7187 (mttt) cc_final: 0.6779 (mttp) REVERT: H 16 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8915 (tp) REVERT: H 46 TRP cc_start: 0.8432 (t-100) cc_final: 0.7854 (t-100) REVERT: H 219 LYS cc_start: 0.7178 (mttt) cc_final: 0.6778 (mttp) outliers start: 88 outliers final: 58 residues processed: 419 average time/residue: 0.1674 time to fit residues: 110.6358 Evaluate side-chains 421 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 33 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 183 ASN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 179 GLN G 183 ASN H 179 GLN H 183 ASN ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.173632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103552 restraints weight = 109504.877| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 5.39 r_work: 0.2772 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23688 Z= 0.179 Angle : 0.583 5.999 32024 Z= 0.303 Chirality : 0.044 0.148 3448 Planarity : 0.003 0.027 4200 Dihedral : 5.260 35.774 3352 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.72 % Allowed : 12.84 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.15), residues: 2912 helix: 0.83 (0.13), residues: 1424 sheet: -0.53 (0.22), residues: 496 loop : -1.34 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 347 TYR 0.009 0.001 TYR H 284 PHE 0.011 0.001 PHE F 99 TRP 0.006 0.001 TRP E 46 HIS 0.006 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (23688) covalent geometry : angle 0.58273 / 0.30 (32024) hydrogen bonds : bond 0.04073 / 2.64 ( 1128) hydrogen bonds : angle 4.28659 / 3.03 ( 3256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 344 time to evaluate : 0.857 Fit side-chains REVERT: A 16 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8788 (tp) REVERT: A 46 TRP cc_start: 0.8262 (t-100) cc_final: 0.7737 (t-100) REVERT: A 219 LYS cc_start: 0.7176 (mttt) cc_final: 0.6767 (mttp) REVERT: A 227 TYR cc_start: 0.8302 (m-80) cc_final: 0.8021 (m-80) REVERT: A 272 MET cc_start: 0.6967 (mmm) cc_final: 0.6377 (mmm) REVERT: B 16 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8789 (tp) REVERT: B 46 TRP cc_start: 0.8276 (t-100) cc_final: 0.7746 (t-100) REVERT: B 219 LYS cc_start: 0.7177 (mttt) cc_final: 0.6767 (mttp) REVERT: B 227 TYR cc_start: 0.8304 (m-80) cc_final: 0.8022 (m-80) REVERT: B 272 MET cc_start: 0.6975 (mmm) cc_final: 0.6384 (mmm) REVERT: C 16 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8792 (tp) REVERT: C 46 TRP cc_start: 0.8257 (t-100) cc_final: 0.7731 (t-100) REVERT: C 194 GLU cc_start: 0.7944 (tp30) cc_final: 0.7540 (mt-10) REVERT: C 219 LYS cc_start: 0.7181 (mttt) cc_final: 0.6769 (mttp) REVERT: C 227 TYR cc_start: 0.8303 (m-80) cc_final: 0.8019 (m-80) REVERT: D 16 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 46 TRP cc_start: 0.8261 (t-100) cc_final: 0.7732 (t-100) REVERT: D 219 LYS cc_start: 0.7168 (mttt) cc_final: 0.6756 (mttp) REVERT: D 227 TYR cc_start: 0.8300 (m-80) cc_final: 0.8018 (m-80) REVERT: D 272 MET cc_start: 0.6978 (mmm) cc_final: 0.6383 (mmm) REVERT: E 16 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8789 (tp) REVERT: E 46 TRP cc_start: 0.8251 (t-100) cc_final: 0.7721 (t-100) REVERT: E 219 LYS cc_start: 0.7173 (mttt) cc_final: 0.6761 (mttp) REVERT: E 227 TYR cc_start: 0.8304 (m-80) cc_final: 0.8020 (m-80) REVERT: F 16 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8790 (tp) REVERT: F 46 TRP cc_start: 0.8264 (t-100) cc_final: 0.7733 (t-100) REVERT: F 194 GLU cc_start: 0.7950 (tp30) cc_final: 0.7544 (mt-10) REVERT: F 219 LYS cc_start: 0.7166 (mttt) cc_final: 0.6756 (mttp) REVERT: F 227 TYR cc_start: 0.8301 (m-80) cc_final: 0.8018 (m-80) REVERT: F 272 MET cc_start: 0.6986 (mmm) cc_final: 0.6398 (mmm) REVERT: G 16 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (tp) REVERT: G 46 TRP cc_start: 0.8249 (t-100) cc_final: 0.7720 (t-100) REVERT: G 219 LYS cc_start: 0.7187 (mttt) cc_final: 0.6775 (mttp) REVERT: G 227 TYR cc_start: 0.8306 (m-80) cc_final: 0.8023 (m-80) REVERT: G 272 MET cc_start: 0.6966 (mmm) cc_final: 0.6380 (mmm) REVERT: H 16 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8789 (tp) REVERT: H 46 TRP cc_start: 0.8258 (t-100) cc_final: 0.7728 (t-100) REVERT: H 219 LYS cc_start: 0.7179 (mttt) cc_final: 0.6770 (mttp) REVERT: H 227 TYR cc_start: 0.8303 (m-80) cc_final: 0.8020 (m-80) REVERT: H 272 MET cc_start: 0.6974 (mmm) cc_final: 0.6382 (mmm) outliers start: 63 outliers final: 39 residues processed: 396 average time/residue: 0.1646 time to fit residues: 102.9004 Evaluate side-chains 405 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 358 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 21 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN ** G 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.170053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.098084 restraints weight = 106046.199| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 5.16 r_work: 0.2726 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 23688 Z= 0.309 Angle : 0.685 6.722 32024 Z= 0.353 Chirality : 0.048 0.157 3448 Planarity : 0.004 0.034 4200 Dihedral : 5.486 39.206 3352 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.79 % Allowed : 12.46 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.15), residues: 2912 helix: 0.65 (0.13), residues: 1424 sheet: -0.58 (0.23), residues: 496 loop : -1.35 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 109 TYR 0.014 0.002 TYR H 284 PHE 0.011 0.002 PHE B 99 TRP 0.008 0.002 TRP B 46 HIS 0.006 0.002 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.31 (23688) covalent geometry : angle 0.68515 / 0.35 (32024) hydrogen bonds : bond 0.05103 / 3.31 ( 1128) hydrogen bonds : angle 4.41785 / 3.13 ( 3256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 382 time to evaluate : 0.974 Fit side-chains REVERT: A 16 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8846 (tt) REVERT: A 46 TRP cc_start: 0.8315 (t-100) cc_final: 0.7770 (t-100) REVERT: A 219 LYS cc_start: 0.7249 (mttt) cc_final: 0.6801 (mttp) REVERT: A 308 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7170 (tptm) REVERT: B 16 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8842 (tt) REVERT: B 46 TRP cc_start: 0.8316 (t-100) cc_final: 0.7770 (t-100) REVERT: B 219 LYS cc_start: 0.7257 (mttt) cc_final: 0.6812 (mttp) REVERT: B 308 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7178 (tptm) REVERT: C 16 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8848 (tt) REVERT: C 46 TRP cc_start: 0.8322 (t-100) cc_final: 0.7758 (t-100) REVERT: C 219 LYS cc_start: 0.7265 (mttt) cc_final: 0.6819 (mttp) REVERT: C 308 LYS cc_start: 0.7813 (ttpt) cc_final: 0.7164 (tptm) REVERT: D 16 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8845 (tt) REVERT: D 46 TRP cc_start: 0.8323 (t-100) cc_final: 0.7756 (t-100) REVERT: D 219 LYS cc_start: 0.7253 (mttt) cc_final: 0.6802 (mttp) REVERT: D 308 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7173 (tptm) REVERT: E 16 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8846 (tt) REVERT: E 46 TRP cc_start: 0.8301 (t-100) cc_final: 0.7757 (t-100) REVERT: E 219 LYS cc_start: 0.7261 (mttt) cc_final: 0.6811 (mttp) REVERT: E 308 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7173 (tptm) REVERT: F 16 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8847 (tt) REVERT: F 46 TRP cc_start: 0.8331 (t-100) cc_final: 0.7761 (t-100) REVERT: F 219 LYS cc_start: 0.7252 (mttt) cc_final: 0.6807 (mttp) REVERT: F 308 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7170 (tptm) REVERT: G 16 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8844 (tt) REVERT: G 46 TRP cc_start: 0.8299 (t-100) cc_final: 0.7749 (t-100) REVERT: G 219 LYS cc_start: 0.7259 (mttt) cc_final: 0.6811 (mttp) REVERT: G 308 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7179 (tptm) REVERT: H 16 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8850 (tt) REVERT: H 46 TRP cc_start: 0.8316 (t-100) cc_final: 0.7767 (t-100) REVERT: H 219 LYS cc_start: 0.7259 (mttt) cc_final: 0.6817 (mttp) REVERT: H 308 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7161 (tptm) outliers start: 88 outliers final: 56 residues processed: 430 average time/residue: 0.1698 time to fit residues: 114.2596 Evaluate side-chains 455 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 391 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 278 optimal weight: 0.5980 chunk 168 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN A 183 ASN B 183 ASN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN ** G 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.179432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120439 restraints weight = 118700.849| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 5.09 r_work: 0.2760 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23688 Z= 0.160 Angle : 0.586 7.750 32024 Z= 0.303 Chirality : 0.044 0.148 3448 Planarity : 0.003 0.029 4200 Dihedral : 5.222 35.421 3352 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.38 % Allowed : 14.13 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.15), residues: 2912 helix: 0.96 (0.13), residues: 1424 sheet: -0.39 (0.23), residues: 496 loop : -1.21 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 364 TYR 0.009 0.001 TYR B 132 PHE 0.011 0.001 PHE B 99 TRP 0.005 0.001 TRP D 46 HIS 0.006 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (23688) covalent geometry : angle 0.58642 / 0.30 (32024) hydrogen bonds : bond 0.03841 / 2.49 ( 1128) hydrogen bonds : angle 4.19721 / 2.96 ( 3256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.872 Fit side-chains REVERT: A 16 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8793 (tp) REVERT: A 46 TRP cc_start: 0.8302 (t-100) cc_final: 0.7722 (t-100) REVERT: A 219 LYS cc_start: 0.7318 (mttt) cc_final: 0.6861 (mttp) REVERT: A 308 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7156 (tptm) REVERT: B 16 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8793 (tp) REVERT: B 46 TRP cc_start: 0.8302 (t-100) cc_final: 0.7719 (t-100) REVERT: B 219 LYS cc_start: 0.7314 (mttt) cc_final: 0.6858 (mttp) REVERT: B 308 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7163 (tptm) REVERT: C 16 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8794 (tp) REVERT: C 46 TRP cc_start: 0.8307 (t-100) cc_final: 0.7729 (t-100) REVERT: C 219 LYS cc_start: 0.7325 (mttt) cc_final: 0.6870 (mttp) REVERT: C 308 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7151 (tptm) REVERT: D 16 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8797 (tp) REVERT: D 46 TRP cc_start: 0.8295 (t-100) cc_final: 0.7708 (t-100) REVERT: D 194 GLU cc_start: 0.7887 (tp30) cc_final: 0.7434 (mt-10) REVERT: D 219 LYS cc_start: 0.7315 (mttt) cc_final: 0.6874 (mttp) REVERT: D 308 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7162 (tptm) REVERT: E 16 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8801 (tp) REVERT: E 46 TRP cc_start: 0.8292 (t-100) cc_final: 0.7710 (t-100) REVERT: E 219 LYS cc_start: 0.7323 (mttt) cc_final: 0.6870 (mttp) REVERT: E 308 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7160 (tptm) REVERT: F 16 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8800 (tp) REVERT: F 46 TRP cc_start: 0.8300 (t-100) cc_final: 0.7718 (t-100) REVERT: F 219 LYS cc_start: 0.7317 (mttt) cc_final: 0.6878 (mttp) REVERT: F 308 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7169 (tptm) REVERT: G 16 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8795 (tp) REVERT: G 46 TRP cc_start: 0.8292 (t-100) cc_final: 0.7710 (t-100) REVERT: G 219 LYS cc_start: 0.7324 (mttt) cc_final: 0.6872 (mttp) REVERT: G 308 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7166 (tptm) REVERT: H 16 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8798 (tp) REVERT: H 46 TRP cc_start: 0.8305 (t-100) cc_final: 0.7721 (t-100) REVERT: H 219 LYS cc_start: 0.7323 (mttt) cc_final: 0.6868 (mttp) REVERT: H 308 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7165 (tptm) outliers start: 55 outliers final: 33 residues processed: 374 average time/residue: 0.1679 time to fit residues: 96.8207 Evaluate side-chains 395 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 77 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 chunk 260 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 134 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN B 183 ASN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.176483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103291 restraints weight = 97218.957| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.59 r_work: 0.2838 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23688 Z= 0.104 Angle : 0.539 7.447 32024 Z= 0.279 Chirality : 0.042 0.141 3448 Planarity : 0.003 0.027 4200 Dihedral : 4.853 32.215 3352 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.78 % Allowed : 15.07 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.15), residues: 2912 helix: 1.25 (0.14), residues: 1424 sheet: -0.09 (0.23), residues: 496 loop : -1.14 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 347 TYR 0.008 0.001 TYR F 132 PHE 0.010 0.001 PHE C 99 TRP 0.002 0.001 TRP D 46 HIS 0.005 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (23688) covalent geometry : angle 0.53947 / 0.28 (32024) hydrogen bonds : bond 0.02993 / 1.94 ( 1128) hydrogen bonds : angle 3.97866 / 2.80 ( 3256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 370 time to evaluate : 0.920 Fit side-chains REVERT: A 46 TRP cc_start: 0.8184 (t-100) cc_final: 0.7689 (t-100) REVERT: A 65 MET cc_start: 0.9310 (mmm) cc_final: 0.8972 (tpt) REVERT: A 194 GLU cc_start: 0.7888 (tp30) cc_final: 0.7473 (mt-10) REVERT: B 46 TRP cc_start: 0.8193 (t-100) cc_final: 0.7692 (t-100) REVERT: B 65 MET cc_start: 0.9318 (mmm) cc_final: 0.8976 (tpt) REVERT: B 194 GLU cc_start: 0.7907 (tp30) cc_final: 0.7475 (mt-10) REVERT: C 46 TRP cc_start: 0.8190 (t-100) cc_final: 0.7695 (t-100) REVERT: C 65 MET cc_start: 0.9314 (mmm) cc_final: 0.8978 (tpt) REVERT: C 194 GLU cc_start: 0.7881 (tp30) cc_final: 0.7464 (mt-10) REVERT: D 46 TRP cc_start: 0.8172 (t-100) cc_final: 0.7670 (t-100) REVERT: D 194 GLU cc_start: 0.7885 (tp30) cc_final: 0.7465 (mt-10) REVERT: E 46 TRP cc_start: 0.8184 (t-100) cc_final: 0.7688 (t-100) REVERT: E 65 MET cc_start: 0.9313 (mmm) cc_final: 0.8974 (tpt) REVERT: E 194 GLU cc_start: 0.7891 (tp30) cc_final: 0.7466 (mt-10) REVERT: F 46 TRP cc_start: 0.8183 (t-100) cc_final: 0.7688 (t-100) REVERT: F 65 MET cc_start: 0.9310 (mmm) cc_final: 0.8970 (tpt) REVERT: F 194 GLU cc_start: 0.7889 (tp30) cc_final: 0.7470 (mt-10) REVERT: G 46 TRP cc_start: 0.8171 (t-100) cc_final: 0.7674 (t-100) REVERT: G 65 MET cc_start: 0.9314 (mmm) cc_final: 0.8975 (tpt) REVERT: G 194 GLU cc_start: 0.7901 (tp30) cc_final: 0.7472 (mt-10) REVERT: H 46 TRP cc_start: 0.8206 (t-100) cc_final: 0.7704 (t-100) REVERT: H 65 MET cc_start: 0.9307 (mmm) cc_final: 0.8965 (tpt) REVERT: H 194 GLU cc_start: 0.7903 (tp30) cc_final: 0.7477 (mt-10) outliers start: 41 outliers final: 23 residues processed: 396 average time/residue: 0.1678 time to fit residues: 105.1355 Evaluate side-chains 391 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 368 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 179 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 chunk 226 optimal weight: 5.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN B 183 ASN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.175975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103733 restraints weight = 99026.453| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.59 r_work: 0.2820 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23688 Z= 0.112 Angle : 0.545 7.493 32024 Z= 0.279 Chirality : 0.042 0.142 3448 Planarity : 0.003 0.026 4200 Dihedral : 4.799 32.690 3352 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.23 % Allowed : 15.92 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.15), residues: 2912 helix: 1.36 (0.14), residues: 1424 sheet: 0.12 (0.23), residues: 496 loop : -1.11 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 347 TYR 0.011 0.001 TYR C 227 PHE 0.008 0.001 PHE H 99 TRP 0.004 0.001 TRP F 46 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (23688) covalent geometry : angle 0.54537 / 0.28 (32024) hydrogen bonds : bond 0.03177 / 2.05 ( 1128) hydrogen bonds : angle 3.93810 / 2.78 ( 3256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 0.877 Fit side-chains REVERT: A 46 TRP cc_start: 0.8226 (t-100) cc_final: 0.7722 (t-100) REVERT: A 194 GLU cc_start: 0.7880 (tp30) cc_final: 0.7382 (mt-10) REVERT: A 219 LYS cc_start: 0.7853 (mptt) cc_final: 0.7633 (mttp) REVERT: B 46 TRP cc_start: 0.8199 (t-100) cc_final: 0.7694 (t-100) REVERT: B 194 GLU cc_start: 0.7885 (tp30) cc_final: 0.7381 (mt-10) REVERT: B 219 LYS cc_start: 0.7860 (mptt) cc_final: 0.7639 (mttp) REVERT: C 46 TRP cc_start: 0.8229 (t-100) cc_final: 0.7725 (t-100) REVERT: C 194 GLU cc_start: 0.7874 (tp30) cc_final: 0.7386 (mt-10) REVERT: C 219 LYS cc_start: 0.7860 (mptt) cc_final: 0.7645 (mttp) REVERT: D 46 TRP cc_start: 0.8200 (t-100) cc_final: 0.7673 (t-100) REVERT: D 194 GLU cc_start: 0.7879 (tp30) cc_final: 0.7382 (mt-10) REVERT: D 219 LYS cc_start: 0.7871 (mptt) cc_final: 0.7653 (mttp) REVERT: E 46 TRP cc_start: 0.8230 (t-100) cc_final: 0.7725 (t-100) REVERT: E 194 GLU cc_start: 0.7872 (tp30) cc_final: 0.7373 (mt-10) REVERT: E 219 LYS cc_start: 0.7848 (mptt) cc_final: 0.7633 (mttp) REVERT: F 46 TRP cc_start: 0.8224 (t-100) cc_final: 0.7719 (t-100) REVERT: F 194 GLU cc_start: 0.7884 (tp30) cc_final: 0.7391 (mt-10) REVERT: F 219 LYS cc_start: 0.7869 (mptt) cc_final: 0.7652 (mttp) REVERT: G 46 TRP cc_start: 0.8180 (t-100) cc_final: 0.7709 (t-100) REVERT: G 194 GLU cc_start: 0.7872 (tp30) cc_final: 0.7373 (mt-10) REVERT: G 219 LYS cc_start: 0.7847 (mptt) cc_final: 0.7628 (mttp) REVERT: H 46 TRP cc_start: 0.8228 (t-100) cc_final: 0.7724 (t-100) REVERT: H 194 GLU cc_start: 0.7886 (tp30) cc_final: 0.7388 (mt-10) REVERT: H 219 LYS cc_start: 0.7860 (mptt) cc_final: 0.7642 (mttp) outliers start: 28 outliers final: 20 residues processed: 378 average time/residue: 0.1611 time to fit residues: 96.7775 Evaluate side-chains 383 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 363 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 117 optimal weight: 4.9990 chunk 215 optimal weight: 0.0050 chunk 30 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 240 optimal weight: 0.0020 chunk 219 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN B 183 ASN C 183 ASN C 352 GLN D 183 ASN E 183 ASN F 183 ASN F 352 GLN G 183 ASN H 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.178491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104924 restraints weight = 106725.382| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.95 r_work: 0.2845 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23688 Z= 0.100 Angle : 0.548 8.147 32024 Z= 0.276 Chirality : 0.042 0.140 3448 Planarity : 0.003 0.027 4200 Dihedral : 4.601 31.021 3352 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.14 % Allowed : 16.01 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.15), residues: 2912 helix: 1.46 (0.14), residues: 1424 sheet: 0.37 (0.23), residues: 496 loop : -1.03 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 347 TYR 0.012 0.001 TYR B 227 PHE 0.009 0.001 PHE F 99 TRP 0.003 0.001 TRP D 46 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (23688) covalent geometry : angle 0.54831 / 0.28 (32024) hydrogen bonds : bond 0.02850 / 1.84 ( 1128) hydrogen bonds : angle 3.84272 / 2.70 ( 3256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6432.38 seconds wall clock time: 110 minutes 48.00 seconds (6648.00 seconds total)