Starting phenix.real_space_refine on Fri Jul 3 19:33:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11mn_75838/07_2026/11mn_75838.cif Found real_map, /net/cci-nas-00/data/ceres_data/11mn_75838/07_2026/11mn_75838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11mn_75838/07_2026/11mn_75838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11mn_75838/07_2026/11mn_75838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11mn_75838/07_2026/11mn_75838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11mn_75838/07_2026/11mn_75838.map" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9440 2.51 5 N 2830 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15490 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1549 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 1.90, per 1000 atoms: 0.12 Number of scatterers: 15490 At special positions: 0 Unit cell: (93.7829, 98.0783, 143.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3120 8.00 N 2830 7.00 C 9440 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: 1.21 Conformation dependent library (CDL) restraints added in 546.8 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.818A pdb=" N ALA A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Proline residue: A 132 - end of helix removed outlier: 3.726A pdb=" N GLU A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 216 removed outlier: 3.545A pdb=" N ASP A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.596A pdb=" N LEU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.851A pdb=" N ARG B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 73 Processing helix chain 'B' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Proline residue: B 132 - end of helix removed outlier: 3.726A pdb=" N GLU B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 216 removed outlier: 3.545A pdb=" N ASP B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 228 removed outlier: 3.596A pdb=" N LEU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.851A pdb=" N ARG C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Proline residue: C 132 - end of helix removed outlier: 3.726A pdb=" N GLU C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.115A pdb=" N LEU C 160 " --> pdb=" O TYR C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 216 removed outlier: 3.546A pdb=" N ASP C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 228 removed outlier: 3.597A pdb=" N LEU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 234 through 249 removed outlier: 3.602A pdb=" N ARG C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 60 removed outlier: 3.850A pdb=" N ARG D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Proline residue: D 132 - end of helix removed outlier: 3.726A pdb=" N GLU D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'D' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 216 removed outlier: 3.545A pdb=" N ASP D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 214 " --> pdb=" O ASN D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 228 removed outlier: 3.596A pdb=" N LEU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.851A pdb=" N ARG E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Proline residue: E 132 - end of helix removed outlier: 3.726A pdb=" N GLU E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU E 160 " --> pdb=" O TYR E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 216 removed outlier: 3.546A pdb=" N ASP E 195 " --> pdb=" O ASN E 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 228 removed outlier: 3.597A pdb=" N LEU E 225 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.851A pdb=" N ARG F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Proline residue: F 132 - end of helix removed outlier: 3.726A pdb=" N GLU F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 156 Processing helix chain 'F' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU F 160 " --> pdb=" O TYR F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 216 removed outlier: 3.545A pdb=" N ASP F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN F 211 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 214 " --> pdb=" O ASN F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 228 removed outlier: 3.596A pdb=" N LEU F 225 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 removed outlier: 3.850A pdb=" N ARG G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY G 98 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Proline residue: G 132 - end of helix removed outlier: 3.726A pdb=" N GLU G 136 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 156 Processing helix chain 'G' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU G 160 " --> pdb=" O TYR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 216 removed outlier: 3.545A pdb=" N ASP G 195 " --> pdb=" O ASN G 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG G 214 " --> pdb=" O ASN G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 228 removed outlier: 3.596A pdb=" N LEU G 225 " --> pdb=" O ASP G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'G' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 60 removed outlier: 3.851A pdb=" N ARG H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Proline residue: H 132 - end of helix removed outlier: 3.726A pdb=" N GLU H 136 " --> pdb=" O PRO H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 156 Processing helix chain 'H' and resid 156 through 161 removed outlier: 4.115A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 216 removed outlier: 3.546A pdb=" N ASP H 195 " --> pdb=" O ASN H 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET H 196 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN H 211 " --> pdb=" O GLN H 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG H 214 " --> pdb=" O ASN H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 228 removed outlier: 3.597A pdb=" N LEU H 225 " --> pdb=" O ASP H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 233 Processing helix chain 'H' and resid 234 through 249 removed outlier: 3.602A pdb=" N ARG H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG H 247 " --> pdb=" O SER H 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 60 removed outlier: 3.850A pdb=" N ARG I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 73 Processing helix chain 'I' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Proline residue: I 132 - end of helix removed outlier: 3.726A pdb=" N GLU I 136 " --> pdb=" O PRO I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 156 Processing helix chain 'I' and resid 156 through 161 removed outlier: 4.115A pdb=" N LEU I 160 " --> pdb=" O TYR I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 216 removed outlier: 3.545A pdb=" N ASP I 195 " --> pdb=" O ASN I 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN I 211 " --> pdb=" O GLN I 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG I 214 " --> pdb=" O ASN I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 228 removed outlier: 3.596A pdb=" N LEU I 225 " --> pdb=" O ASP I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG I 240 " --> pdb=" O GLY I 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG I 247 " --> pdb=" O SER I 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 60 removed outlier: 3.851A pdb=" N ARG J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 86 through 143 removed outlier: 4.556A pdb=" N ALA J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Proline residue: J 132 - end of helix removed outlier: 3.726A pdb=" N GLU J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 156 Processing helix chain 'J' and resid 156 through 161 removed outlier: 4.116A pdb=" N LEU J 160 " --> pdb=" O TYR J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 216 removed outlier: 3.546A pdb=" N ASP J 195 " --> pdb=" O ASN J 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET J 196 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN J 211 " --> pdb=" O GLN J 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG J 214 " --> pdb=" O ASN J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 228 removed outlier: 3.597A pdb=" N LEU J 225 " --> pdb=" O ASP J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 234 through 249 removed outlier: 3.601A pdb=" N ARG J 240 " --> pdb=" O GLY J 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER J 243 " --> pdb=" O SER J 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG J 247 " --> pdb=" O SER J 243 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3780 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: 2.47 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5570 1.35 - 1.46: 3267 1.46 - 1.58: 6663 1.58 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 15700 Sorted by residual: bond pdb=" CG LEU A 101 " pdb=" CD1 LEU A 101 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CG LEU F 101 " pdb=" CD1 LEU F 101 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CG LEU I 101 " pdb=" CD1 LEU I 101 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CG LEU D 101 " pdb=" CD1 LEU D 101 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CG LEU C 101 " pdb=" CD1 LEU C 101 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 ... (remaining 15695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 20768 2.09 - 4.19: 362 4.19 - 6.28: 30 6.28 - 8.37: 50 8.37 - 10.47: 20 Bond angle restraints: 21230 Sorted by residual: angle pdb=" CA ARG B 114 " pdb=" CB ARG B 114 " pdb=" CG ARG B 114 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA ARG I 114 " pdb=" CB ARG I 114 " pdb=" CG ARG I 114 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA ARG C 114 " pdb=" CB ARG C 114 " pdb=" CG ARG C 114 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA ARG H 114 " pdb=" CB ARG H 114 " pdb=" CG ARG H 114 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA ARG D 114 " pdb=" CB ARG D 114 " pdb=" CG ARG D 114 " ideal model delta sigma weight residual 114.10 121.24 -7.14 2.00e+00 2.50e-01 1.27e+01 ... (remaining 21225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 8270 15.21 - 30.41: 1100 30.41 - 45.62: 260 45.62 - 60.83: 20 60.83 - 76.03: 40 Dihedral angle restraints: 9690 sinusoidal: 3780 harmonic: 5910 Sorted by residual: dihedral pdb=" CA THR F 113 " pdb=" C THR F 113 " pdb=" N ARG F 114 " pdb=" CA ARG F 114 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA THR A 113 " pdb=" C THR A 113 " pdb=" N ARG A 114 " pdb=" CA ARG A 114 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA THR D 113 " pdb=" C THR D 113 " pdb=" N ARG D 114 " pdb=" CA ARG D 114 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 9687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1604 0.032 - 0.064: 460 0.064 - 0.096: 155 0.096 - 0.128: 41 0.128 - 0.160: 30 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CG LEU F 134 " pdb=" CB LEU F 134 " pdb=" CD1 LEU F 134 " pdb=" CD2 LEU F 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CG LEU A 134 " pdb=" CB LEU A 134 " pdb=" CD1 LEU A 134 " pdb=" CD2 LEU A 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CG LEU G 134 " pdb=" CB LEU G 134 " pdb=" CD1 LEU G 134 " pdb=" CD2 LEU G 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 2287 not shown) Planarity restraints: 2930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 247 " -0.157 9.50e-02 1.11e+02 7.11e-02 4.27e+00 pdb=" NE ARG J 247 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 247 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG J 247 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 247 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 247 " -0.157 9.50e-02 1.11e+02 7.11e-02 4.26e+00 pdb=" NE ARG D 247 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 247 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG D 247 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 247 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 247 " -0.157 9.50e-02 1.11e+02 7.11e-02 4.26e+00 pdb=" NE ARG I 247 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG I 247 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG I 247 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG I 247 " 0.001 2.00e-02 2.50e+03 ... (remaining 2927 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3576 2.78 - 3.31: 16296 3.31 - 3.84: 25409 3.84 - 4.37: 31751 4.37 - 4.90: 52808 Nonbonded interactions: 129840 Sorted by model distance: nonbonded pdb=" O ASN D 109 " pdb=" OG1 THR D 113 " model vdw 2.247 3.040 nonbonded pdb=" O ASN I 109 " pdb=" OG1 THR I 113 " model vdw 2.247 3.040 nonbonded pdb=" O ASN H 109 " pdb=" OG1 THR H 113 " model vdw 2.247 3.040 nonbonded pdb=" O ASN C 109 " pdb=" OG1 THR C 113 " model vdw 2.247 3.040 nonbonded pdb=" O ASN J 109 " pdb=" OG1 THR J 113 " model vdw 2.248 3.040 ... (remaining 129835 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: 0.06 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' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15700 Z= 0.146 Angle : 0.783 10.468 21230 Z= 0.385 Chirality : 0.039 0.160 2290 Planarity : 0.006 0.071 2930 Dihedral : 14.879 76.034 5910 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.27 % Allowed : 12.74 % Favored : 85.99 % 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: -1.23 (0.17), residues: 2020 helix: -0.94 (0.11), residues: 1630 sheet: None (None), residues: 0 loop : 0.76 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 247 TYR 0.006 0.001 TYR D 67 PHE 0.005 0.001 PHE G 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (15700) covalent geometry : angle 0.78292 / 0.38 (21230) hydrogen bonds : bond 0.26548 / 17.72 ( 1280) hydrogen bonds : angle 7.92729 / 5.64 ( 3780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.9018 (mmm) cc_final: 0.8607 (mmm) REVERT: A 198 ASN cc_start: 0.8789 (m-40) cc_final: 0.8326 (m110) REVERT: B 198 ASN cc_start: 0.8807 (m-40) cc_final: 0.8306 (m110) REVERT: C 198 ASN cc_start: 0.8789 (m-40) cc_final: 0.8306 (m110) REVERT: D 198 ASN cc_start: 0.8800 (m-40) cc_final: 0.8455 (m110) REVERT: E 198 ASN cc_start: 0.8797 (m-40) cc_final: 0.8451 (m110) REVERT: F 172 MET cc_start: 0.9027 (mmm) cc_final: 0.8613 (mmm) REVERT: F 198 ASN cc_start: 0.8785 (m-40) cc_final: 0.8327 (m110) REVERT: G 198 ASN cc_start: 0.8818 (m-40) cc_final: 0.8311 (m110) REVERT: H 198 ASN cc_start: 0.8798 (m-40) cc_final: 0.8329 (m110) REVERT: I 198 ASN cc_start: 0.8787 (m-40) cc_final: 0.8447 (m110) REVERT: J 198 ASN cc_start: 0.8787 (m-40) cc_final: 0.8451 (m110) outliers start: 20 outliers final: 10 residues processed: 307 average time/residue: 0.1104 time to fit residues: 52.4514 Evaluate side-chains 261 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain J residue 194 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 124 ASN C 124 ASN E 124 ASN F 124 ASN G 124 ASN H 124 ASN I 124 ASN J 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066404 restraints weight = 40313.668| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.64 r_work: 0.2989 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15700 Z= 0.154 Angle : 0.591 7.256 21230 Z= 0.300 Chirality : 0.038 0.129 2290 Planarity : 0.004 0.027 2930 Dihedral : 3.914 13.298 2290 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.27 % Allowed : 12.93 % Favored : 85.80 % 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: 1.85 (0.18), residues: 2020 helix: 1.55 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : 0.14 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 247 TYR 0.009 0.001 TYR J 67 PHE 0.005 0.001 PHE E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15700) covalent geometry : angle 0.59081 / 0.30 (21230) hydrogen bonds : bond 0.03745 / 2.54 ( 1280) hydrogen bonds : angle 3.74625 / 2.68 ( 3780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8978 (m-40) cc_final: 0.8542 (m110) REVERT: B 59 MET cc_start: 0.8615 (mmt) cc_final: 0.8121 (mmt) REVERT: B 198 ASN cc_start: 0.8971 (m-40) cc_final: 0.8540 (m110) REVERT: C 66 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 136 GLU cc_start: 0.8695 (tp30) cc_final: 0.8464 (tp30) REVERT: C 198 ASN cc_start: 0.8982 (m-40) cc_final: 0.8553 (m110) REVERT: E 136 GLU cc_start: 0.8682 (tp30) cc_final: 0.8424 (tp30) REVERT: F 198 ASN cc_start: 0.8984 (m-40) cc_final: 0.8546 (m110) REVERT: G 59 MET cc_start: 0.8595 (mmt) cc_final: 0.8110 (mmt) REVERT: G 66 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8306 (mm-30) REVERT: G 198 ASN cc_start: 0.8971 (m-40) cc_final: 0.8538 (m110) REVERT: H 66 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8410 (mm-30) REVERT: H 136 GLU cc_start: 0.8686 (tp30) cc_final: 0.8450 (tp30) REVERT: H 198 ASN cc_start: 0.8982 (m-40) cc_final: 0.8549 (m110) REVERT: J 136 GLU cc_start: 0.8683 (tp30) cc_final: 0.8427 (tp30) outliers start: 20 outliers final: 5 residues processed: 288 average time/residue: 0.0884 time to fit residues: 41.7148 Evaluate side-chains 257 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain H residue 209 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 GLN D 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065702 restraints weight = 40492.129| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.65 r_work: 0.2965 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15700 Z= 0.157 Angle : 0.561 7.449 21230 Z= 0.279 Chirality : 0.038 0.127 2290 Planarity : 0.003 0.020 2930 Dihedral : 3.703 17.384 2280 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.61 % Allowed : 12.04 % Favored : 85.35 % 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: 3.13 (0.19), residues: 2020 helix: 2.49 (0.12), residues: 1630 sheet: None (None), residues: 0 loop : 0.30 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 247 TYR 0.009 0.001 TYR J 67 PHE 0.006 0.001 PHE A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (15700) covalent geometry : angle 0.56063 / 0.28 (21230) hydrogen bonds : bond 0.03452 / 2.34 ( 1280) hydrogen bonds : angle 3.34270 / 2.39 ( 3780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.609 Fit side-chains REVERT: A 66 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8456 (mm-30) REVERT: A 172 MET cc_start: 0.9339 (mmm) cc_final: 0.8800 (mmm) REVERT: A 198 ASN cc_start: 0.8960 (m-40) cc_final: 0.8554 (m110) REVERT: A 242 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8324 (mm) REVERT: B 59 MET cc_start: 0.8544 (mmt) cc_final: 0.8025 (mmt) REVERT: B 66 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 183 ILE cc_start: 0.8884 (mt) cc_final: 0.8680 (mm) REVERT: B 198 ASN cc_start: 0.8946 (m-40) cc_final: 0.8522 (m110) REVERT: B 242 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8254 (mm) REVERT: C 136 GLU cc_start: 0.8678 (tp30) cc_final: 0.8229 (tp30) REVERT: C 183 ILE cc_start: 0.8853 (mt) cc_final: 0.8631 (mm) REVERT: C 198 ASN cc_start: 0.8973 (m-40) cc_final: 0.8556 (m110) REVERT: D 198 ASN cc_start: 0.8912 (m-40) cc_final: 0.8509 (m110) REVERT: E 136 GLU cc_start: 0.8670 (tp30) cc_final: 0.8393 (tp30) REVERT: E 198 ASN cc_start: 0.8923 (m-40) cc_final: 0.8503 (m110) REVERT: E 242 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8395 (mm) REVERT: F 66 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8457 (mm-30) REVERT: F 172 MET cc_start: 0.9340 (mmm) cc_final: 0.8780 (mmm) REVERT: F 198 ASN cc_start: 0.8961 (m-40) cc_final: 0.8555 (m110) REVERT: F 242 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8302 (mm) REVERT: G 59 MET cc_start: 0.8546 (mmt) cc_final: 0.8036 (mmt) REVERT: G 198 ASN cc_start: 0.8944 (m-40) cc_final: 0.8513 (m110) REVERT: G 242 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8212 (mm) REVERT: H 108 GLN cc_start: 0.8350 (tp40) cc_final: 0.8097 (tm-30) REVERT: H 136 GLU cc_start: 0.8686 (tp30) cc_final: 0.8241 (tp30) REVERT: H 183 ILE cc_start: 0.8844 (mt) cc_final: 0.8619 (mm) REVERT: H 198 ASN cc_start: 0.8974 (m-40) cc_final: 0.8561 (m110) REVERT: I 198 ASN cc_start: 0.8907 (m-40) cc_final: 0.8506 (m110) REVERT: J 136 GLU cc_start: 0.8664 (tp30) cc_final: 0.8383 (tp30) REVERT: J 198 ASN cc_start: 0.8933 (m-40) cc_final: 0.8511 (m110) REVERT: J 242 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (mm) outliers start: 41 outliers final: 21 residues processed: 310 average time/residue: 0.1161 time to fit residues: 54.7080 Evaluate side-chains 290 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 107 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN D 108 GLN E 108 GLN E 211 ASN F 108 GLN H 108 GLN I 108 GLN ** J 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067331 restraints weight = 40419.886| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.58 r_work: 0.3022 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15700 Z= 0.160 Angle : 0.560 7.970 21230 Z= 0.274 Chirality : 0.038 0.140 2290 Planarity : 0.003 0.023 2930 Dihedral : 3.587 14.912 2280 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.18 % Allowed : 12.99 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.61 (0.19), residues: 2020 helix: 2.92 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 247 TYR 0.010 0.001 TYR G 67 PHE 0.007 0.001 PHE H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (15700) covalent geometry : angle 0.55954 / 0.27 (21230) hydrogen bonds : bond 0.03278 / 2.23 ( 1280) hydrogen bonds : angle 3.21637 / 2.29 ( 3780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.590 Fit side-chains REVERT: A 172 MET cc_start: 0.9316 (mmm) cc_final: 0.8719 (mmm) REVERT: A 198 ASN cc_start: 0.8947 (m-40) cc_final: 0.8563 (m110) REVERT: A 242 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (mm) REVERT: B 59 MET cc_start: 0.8564 (mmt) cc_final: 0.8092 (mmt) REVERT: B 198 ASN cc_start: 0.8922 (m-40) cc_final: 0.8501 (m110) REVERT: B 242 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8278 (mm) REVERT: C 136 GLU cc_start: 0.8618 (tp30) cc_final: 0.8212 (tp30) REVERT: C 198 ASN cc_start: 0.8939 (m-40) cc_final: 0.8512 (m110) REVERT: D 136 GLU cc_start: 0.8667 (tp30) cc_final: 0.8421 (tp30) REVERT: D 198 ASN cc_start: 0.8823 (m-40) cc_final: 0.8434 (m110) REVERT: E 136 GLU cc_start: 0.8628 (tp30) cc_final: 0.8365 (tp30) REVERT: E 198 ASN cc_start: 0.8883 (m-40) cc_final: 0.8496 (m110) REVERT: E 242 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8394 (mm) REVERT: F 172 MET cc_start: 0.9322 (mmm) cc_final: 0.8724 (mmm) REVERT: F 198 ASN cc_start: 0.8935 (m-40) cc_final: 0.8551 (m110) REVERT: F 242 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8349 (mm) REVERT: G 59 MET cc_start: 0.8560 (mmt) cc_final: 0.8086 (mmt) REVERT: G 198 ASN cc_start: 0.8922 (m-40) cc_final: 0.8517 (m110) REVERT: G 242 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8284 (mm) REVERT: H 136 GLU cc_start: 0.8623 (tp30) cc_final: 0.8217 (tp30) REVERT: H 198 ASN cc_start: 0.8930 (m-40) cc_final: 0.8504 (m110) REVERT: I 136 GLU cc_start: 0.8681 (tp30) cc_final: 0.8434 (tp30) REVERT: I 198 ASN cc_start: 0.8807 (m-40) cc_final: 0.8423 (m110) REVERT: J 136 GLU cc_start: 0.8688 (tp30) cc_final: 0.8440 (tp30) REVERT: J 198 ASN cc_start: 0.8888 (m-40) cc_final: 0.8505 (m110) REVERT: J 242 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (mm) outliers start: 50 outliers final: 32 residues processed: 297 average time/residue: 0.1151 time to fit residues: 53.0603 Evaluate side-chains 289 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 64 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 114 optimal weight: 0.0270 chunk 4 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 191 optimal weight: 0.4980 chunk 182 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN B 211 ASN C 108 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN D 117 ASN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN G 211 ASN H 108 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN I 117 ASN I 211 ASN J 117 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068358 restraints weight = 40248.118| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.67 r_work: 0.3041 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15700 Z= 0.120 Angle : 0.541 7.305 21230 Z= 0.265 Chirality : 0.036 0.129 2290 Planarity : 0.003 0.024 2930 Dihedral : 3.475 14.773 2280 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.80 % Allowed : 13.57 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.90 (0.19), residues: 2020 helix: 3.08 (0.12), residues: 1630 sheet: None (None), residues: 0 loop : 0.29 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 247 TYR 0.010 0.001 TYR B 67 PHE 0.005 0.001 PHE A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15700) covalent geometry : angle 0.54105 / 0.26 (21230) hydrogen bonds : bond 0.02992 / 2.03 ( 1280) hydrogen bonds : angle 3.12632 / 2.23 ( 3780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 0.590 Fit side-chains REVERT: A 66 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8333 (mp0) REVERT: A 172 MET cc_start: 0.9287 (mmm) cc_final: 0.8680 (mmm) REVERT: A 198 ASN cc_start: 0.8929 (m-40) cc_final: 0.8547 (m110) REVERT: A 242 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 59 MET cc_start: 0.8496 (mmt) cc_final: 0.7986 (mmt) REVERT: B 66 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8353 (mp0) REVERT: B 198 ASN cc_start: 0.8897 (m-40) cc_final: 0.8510 (m110) REVERT: B 242 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8277 (mm) REVERT: C 136 GLU cc_start: 0.8608 (tp30) cc_final: 0.8204 (tp30) REVERT: C 198 ASN cc_start: 0.8918 (m-40) cc_final: 0.8505 (m110) REVERT: D 66 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8160 (mp0) REVERT: D 136 GLU cc_start: 0.8674 (tp30) cc_final: 0.8426 (tp30) REVERT: D 198 ASN cc_start: 0.8815 (m-40) cc_final: 0.8432 (m110) REVERT: E 136 GLU cc_start: 0.8639 (tp30) cc_final: 0.8385 (tp30) REVERT: E 198 ASN cc_start: 0.8869 (m-40) cc_final: 0.8481 (m110) REVERT: E 242 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8369 (mm) REVERT: F 66 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8337 (mp0) REVERT: F 172 MET cc_start: 0.9306 (mmm) cc_final: 0.8677 (mmm) REVERT: F 198 ASN cc_start: 0.8936 (m-40) cc_final: 0.8547 (m110) REVERT: F 242 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8353 (mm) REVERT: G 59 MET cc_start: 0.8514 (mmt) cc_final: 0.8012 (mmt) REVERT: G 198 ASN cc_start: 0.8914 (m-40) cc_final: 0.8521 (m110) REVERT: G 242 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8300 (mm) REVERT: H 136 GLU cc_start: 0.8612 (tp30) cc_final: 0.8210 (tp30) REVERT: H 198 ASN cc_start: 0.8921 (m-40) cc_final: 0.8507 (m110) REVERT: I 66 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8157 (mp0) REVERT: I 136 GLU cc_start: 0.8686 (tp30) cc_final: 0.8435 (tp30) REVERT: I 198 ASN cc_start: 0.8813 (m-40) cc_final: 0.8427 (m110) REVERT: J 136 GLU cc_start: 0.8628 (tp30) cc_final: 0.8400 (tp30) REVERT: J 198 ASN cc_start: 0.8868 (m-40) cc_final: 0.8481 (m110) REVERT: J 242 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (mm) outliers start: 44 outliers final: 31 residues processed: 293 average time/residue: 0.1196 time to fit residues: 53.3200 Evaluate side-chains 291 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 0.8980 chunk 89 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066749 restraints weight = 39978.345| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.57 r_work: 0.3006 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15700 Z= 0.166 Angle : 0.561 6.408 21230 Z= 0.276 Chirality : 0.038 0.142 2290 Planarity : 0.003 0.023 2930 Dihedral : 3.449 15.239 2280 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.93 % Allowed : 14.39 % Favored : 82.68 % 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: 3.82 (0.19), residues: 2020 helix: 3.06 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : 0.11 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 247 TYR 0.009 0.001 TYR E 67 PHE 0.008 0.001 PHE C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (15700) covalent geometry : angle 0.56128 / 0.28 (21230) hydrogen bonds : bond 0.03206 / 2.18 ( 1280) hydrogen bonds : angle 3.15497 / 2.25 ( 3780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 0.624 Fit side-chains REVERT: A 198 ASN cc_start: 0.8936 (m-40) cc_final: 0.8540 (m110) REVERT: A 242 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 59 MET cc_start: 0.8546 (mmt) cc_final: 0.8055 (mmt) REVERT: B 136 GLU cc_start: 0.8653 (tp30) cc_final: 0.8415 (tp30) REVERT: B 198 ASN cc_start: 0.8874 (m-40) cc_final: 0.8467 (m110) REVERT: B 242 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8282 (mm) REVERT: C 136 GLU cc_start: 0.8625 (tp30) cc_final: 0.8215 (tp30) REVERT: C 198 ASN cc_start: 0.8908 (m-40) cc_final: 0.8480 (m110) REVERT: D 136 GLU cc_start: 0.8691 (tp30) cc_final: 0.8422 (tp30) REVERT: D 198 ASN cc_start: 0.8794 (m-40) cc_final: 0.8419 (m110) REVERT: E 136 GLU cc_start: 0.8649 (tp30) cc_final: 0.8400 (tp30) REVERT: E 198 ASN cc_start: 0.8867 (m-40) cc_final: 0.8472 (m110) REVERT: E 242 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8368 (mm) REVERT: F 198 ASN cc_start: 0.8934 (m-40) cc_final: 0.8534 (m110) REVERT: F 242 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8354 (mm) REVERT: G 59 MET cc_start: 0.8529 (mmt) cc_final: 0.8041 (mmt) REVERT: G 136 GLU cc_start: 0.8668 (tp30) cc_final: 0.8438 (tp30) REVERT: G 198 ASN cc_start: 0.8871 (m-40) cc_final: 0.8460 (m110) REVERT: G 242 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8307 (mm) REVERT: H 136 GLU cc_start: 0.8648 (tp30) cc_final: 0.8239 (tp30) REVERT: H 198 ASN cc_start: 0.8908 (m-40) cc_final: 0.8490 (m110) REVERT: I 136 GLU cc_start: 0.8722 (tp30) cc_final: 0.8450 (tp30) REVERT: I 198 ASN cc_start: 0.8792 (m-40) cc_final: 0.8418 (m110) REVERT: J 136 GLU cc_start: 0.8654 (tp30) cc_final: 0.8420 (tp30) REVERT: J 198 ASN cc_start: 0.8866 (m-40) cc_final: 0.8471 (m110) REVERT: J 242 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8359 (mm) outliers start: 46 outliers final: 34 residues processed: 277 average time/residue: 0.1028 time to fit residues: 45.1185 Evaluate side-chains 295 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 10 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN B 117 ASN C 108 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 117 ASN H 108 GLN H 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067577 restraints weight = 39663.681| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.58 r_work: 0.3023 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15700 Z= 0.137 Angle : 0.533 6.987 21230 Z= 0.260 Chirality : 0.037 0.133 2290 Planarity : 0.003 0.024 2930 Dihedral : 3.400 15.296 2280 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 3.31 % Allowed : 14.01 % Favored : 82.68 % 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: 4.00 (0.19), residues: 2020 helix: 3.14 (0.12), residues: 1630 sheet: None (None), residues: 0 loop : 0.33 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 247 TYR 0.011 0.001 TYR E 141 PHE 0.006 0.001 PHE H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15700) covalent geometry : angle 0.53274 / 0.26 (21230) hydrogen bonds : bond 0.03046 / 2.08 ( 1280) hydrogen bonds : angle 3.10133 / 2.21 ( 3780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.621 Fit side-chains REVERT: A 66 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8289 (mp0) REVERT: A 198 ASN cc_start: 0.8930 (m-40) cc_final: 0.8535 (m110) REVERT: B 59 MET cc_start: 0.8517 (mmt) cc_final: 0.8040 (mmt) REVERT: B 136 GLU cc_start: 0.8649 (tp30) cc_final: 0.8406 (tp30) REVERT: B 198 ASN cc_start: 0.8871 (m-40) cc_final: 0.8489 (m110) REVERT: B 242 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8289 (mm) REVERT: C 136 GLU cc_start: 0.8598 (tp30) cc_final: 0.8329 (tp30) REVERT: C 198 ASN cc_start: 0.8911 (m-40) cc_final: 0.8500 (m110) REVERT: D 66 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8187 (mp0) REVERT: D 136 GLU cc_start: 0.8711 (tp30) cc_final: 0.8448 (tp30) REVERT: D 198 ASN cc_start: 0.8795 (m-40) cc_final: 0.8437 (m110) REVERT: E 59 MET cc_start: 0.8611 (mmt) cc_final: 0.8037 (mmt) REVERT: E 136 GLU cc_start: 0.8614 (tp30) cc_final: 0.8392 (tp30) REVERT: E 198 ASN cc_start: 0.8859 (m-40) cc_final: 0.8486 (m110) REVERT: E 242 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8359 (mm) REVERT: F 66 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8291 (mp0) REVERT: F 198 ASN cc_start: 0.8924 (m-40) cc_final: 0.8526 (m110) REVERT: F 242 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8362 (mm) REVERT: G 59 MET cc_start: 0.8513 (mmt) cc_final: 0.8024 (mmt) REVERT: G 136 GLU cc_start: 0.8661 (tp30) cc_final: 0.8432 (tp30) REVERT: G 198 ASN cc_start: 0.8875 (m-40) cc_final: 0.8491 (m110) REVERT: G 242 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8306 (mm) REVERT: H 136 GLU cc_start: 0.8635 (tp30) cc_final: 0.8244 (tp30) REVERT: H 198 ASN cc_start: 0.8913 (m-40) cc_final: 0.8504 (m110) REVERT: I 66 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8180 (mp0) REVERT: I 136 GLU cc_start: 0.8722 (tp30) cc_final: 0.8458 (tp30) REVERT: I 198 ASN cc_start: 0.8777 (m-40) cc_final: 0.8419 (m110) REVERT: J 59 MET cc_start: 0.8578 (mmt) cc_final: 0.8044 (mmt) REVERT: J 136 GLU cc_start: 0.8645 (tp30) cc_final: 0.8418 (tp30) REVERT: J 198 ASN cc_start: 0.8864 (m-40) cc_final: 0.8490 (m110) REVERT: J 242 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (mm) outliers start: 52 outliers final: 37 residues processed: 273 average time/residue: 0.1050 time to fit residues: 45.6542 Evaluate side-chains 298 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 177 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067653 restraints weight = 40144.088| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.65 r_work: 0.3016 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15700 Z= 0.136 Angle : 0.548 7.901 21230 Z= 0.266 Chirality : 0.037 0.163 2290 Planarity : 0.003 0.030 2930 Dihedral : 3.399 13.406 2280 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.74 % Allowed : 14.59 % Favored : 82.68 % 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: 4.01 (0.19), residues: 2020 helix: 3.15 (0.12), residues: 1630 sheet: None (None), residues: 0 loop : 0.34 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 247 TYR 0.011 0.001 TYR B 67 PHE 0.006 0.001 PHE C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15700) covalent geometry : angle 0.54789 / 0.27 (21230) hydrogen bonds : bond 0.03069 / 2.09 ( 1280) hydrogen bonds : angle 3.11532 / 2.21 ( 3780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8298 (mp0) REVERT: A 198 ASN cc_start: 0.8936 (m-40) cc_final: 0.8520 (m110) REVERT: B 59 MET cc_start: 0.8551 (mmt) cc_final: 0.8052 (mmt) REVERT: B 63 ASP cc_start: 0.7757 (t0) cc_final: 0.7401 (t0) REVERT: B 66 GLU cc_start: 0.8145 (mp0) cc_final: 0.7348 (mp0) REVERT: B 136 GLU cc_start: 0.8710 (tp30) cc_final: 0.8463 (tp30) REVERT: B 198 ASN cc_start: 0.8872 (m-40) cc_final: 0.8466 (m110) REVERT: B 242 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8260 (mm) REVERT: C 136 GLU cc_start: 0.8644 (tp30) cc_final: 0.8245 (tp30) REVERT: C 148 LYS cc_start: 0.9469 (mttt) cc_final: 0.9255 (mtpt) REVERT: C 198 ASN cc_start: 0.8913 (m-40) cc_final: 0.8488 (m110) REVERT: D 136 GLU cc_start: 0.8746 (tp30) cc_final: 0.8468 (tp30) REVERT: D 198 ASN cc_start: 0.8811 (m-40) cc_final: 0.8444 (m110) REVERT: E 136 GLU cc_start: 0.8642 (tp30) cc_final: 0.8411 (tp30) REVERT: E 172 MET cc_start: 0.9357 (mmm) cc_final: 0.9055 (mmm) REVERT: E 198 ASN cc_start: 0.8861 (m-40) cc_final: 0.8465 (m110) REVERT: E 242 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8345 (mm) REVERT: F 66 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8293 (mp0) REVERT: F 172 MET cc_start: 0.9333 (mmm) cc_final: 0.8415 (mmm) REVERT: F 198 ASN cc_start: 0.8935 (m-40) cc_final: 0.8532 (m110) REVERT: F 242 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8348 (mm) REVERT: G 59 MET cc_start: 0.8531 (mmt) cc_final: 0.8038 (mmt) REVERT: G 136 GLU cc_start: 0.8713 (tp30) cc_final: 0.8468 (tp30) REVERT: G 198 ASN cc_start: 0.8870 (m-40) cc_final: 0.8460 (m110) REVERT: G 242 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8262 (mm) REVERT: H 136 GLU cc_start: 0.8675 (tp30) cc_final: 0.8276 (tp30) REVERT: H 198 ASN cc_start: 0.8912 (m-40) cc_final: 0.8493 (m110) REVERT: I 136 GLU cc_start: 0.8745 (tp30) cc_final: 0.8467 (tp30) REVERT: I 198 ASN cc_start: 0.8791 (m-40) cc_final: 0.8427 (m110) REVERT: J 59 MET cc_start: 0.8577 (mmt) cc_final: 0.8027 (mmt) REVERT: J 136 GLU cc_start: 0.8679 (tp30) cc_final: 0.8444 (tp30) REVERT: J 198 ASN cc_start: 0.8867 (m-40) cc_final: 0.8470 (m110) REVERT: J 242 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8319 (mm) outliers start: 43 outliers final: 33 residues processed: 274 average time/residue: 0.0983 time to fit residues: 43.4769 Evaluate side-chains 292 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064620 restraints weight = 40304.759| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.58 r_work: 0.2953 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15700 Z= 0.250 Angle : 0.653 8.201 21230 Z= 0.320 Chirality : 0.041 0.164 2290 Planarity : 0.004 0.027 2930 Dihedral : 3.569 16.077 2280 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.80 % Allowed : 14.59 % Favored : 82.61 % 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: 3.53 (0.19), residues: 2020 helix: 2.77 (0.12), residues: 1650 sheet: None (None), residues: 0 loop : 0.26 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 247 TYR 0.013 0.001 TYR H 141 PHE 0.010 0.002 PHE C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 (15700) covalent geometry : angle 0.65250 / 0.32 (21230) hydrogen bonds : bond 0.03608 / 2.46 ( 1280) hydrogen bonds : angle 3.32604 / 2.36 ( 3780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.9333 (mmm) cc_final: 0.8510 (mmm) REVERT: A 198 ASN cc_start: 0.8949 (m-40) cc_final: 0.8518 (m110) REVERT: B 59 MET cc_start: 0.8612 (mmt) cc_final: 0.8109 (mmt) REVERT: B 63 ASP cc_start: 0.7924 (t0) cc_final: 0.7519 (t0) REVERT: B 66 GLU cc_start: 0.8240 (mp0) cc_final: 0.7398 (mp0) REVERT: B 136 GLU cc_start: 0.8768 (tp30) cc_final: 0.8511 (tp30) REVERT: B 198 ASN cc_start: 0.8902 (m-40) cc_final: 0.8495 (m110) REVERT: B 242 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8250 (mm) REVERT: C 136 GLU cc_start: 0.8747 (tp30) cc_final: 0.8450 (tp30) REVERT: C 198 ASN cc_start: 0.8902 (m-40) cc_final: 0.8466 (m110) REVERT: D 136 GLU cc_start: 0.8772 (tp30) cc_final: 0.8465 (tp30) REVERT: D 198 ASN cc_start: 0.8843 (m-40) cc_final: 0.8466 (m110) REVERT: E 136 GLU cc_start: 0.8733 (tp30) cc_final: 0.8481 (tp30) REVERT: E 198 ASN cc_start: 0.8881 (m-40) cc_final: 0.8469 (m110) REVERT: E 242 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8321 (mm) REVERT: F 172 MET cc_start: 0.9343 (mmm) cc_final: 0.8478 (mmm) REVERT: F 198 ASN cc_start: 0.8953 (m-40) cc_final: 0.8522 (m110) REVERT: F 242 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8308 (mm) REVERT: G 59 MET cc_start: 0.8610 (mmt) cc_final: 0.8112 (mmt) REVERT: G 136 GLU cc_start: 0.8774 (tp30) cc_final: 0.8509 (tp30) REVERT: G 198 ASN cc_start: 0.8892 (m-40) cc_final: 0.8481 (m110) REVERT: G 242 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8261 (mm) REVERT: H 136 GLU cc_start: 0.8748 (tp30) cc_final: 0.8452 (tp30) REVERT: H 198 ASN cc_start: 0.8906 (m-40) cc_final: 0.8453 (m110) REVERT: H 242 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8491 (mm) REVERT: I 136 GLU cc_start: 0.8786 (tp30) cc_final: 0.8483 (tp30) REVERT: I 198 ASN cc_start: 0.8824 (m-40) cc_final: 0.8451 (m110) REVERT: J 136 GLU cc_start: 0.8751 (tp30) cc_final: 0.8481 (tp30) REVERT: J 198 ASN cc_start: 0.8892 (m-40) cc_final: 0.8481 (m110) REVERT: J 242 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8284 (mm) outliers start: 44 outliers final: 35 residues processed: 264 average time/residue: 0.0989 time to fit residues: 42.1775 Evaluate side-chains 288 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 156 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 161 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067246 restraints weight = 39991.411| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.63 r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15700 Z= 0.140 Angle : 0.575 8.731 21230 Z= 0.279 Chirality : 0.038 0.142 2290 Planarity : 0.003 0.028 2930 Dihedral : 3.469 14.413 2280 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.36 % Allowed : 14.90 % Favored : 82.74 % 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: 3.89 (0.19), residues: 2020 helix: 3.06 (0.12), residues: 1630 sheet: None (None), residues: 0 loop : 0.33 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 247 TYR 0.011 0.001 TYR B 67 PHE 0.005 0.001 PHE J 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15700) covalent geometry : angle 0.57541 / 0.28 (21230) hydrogen bonds : bond 0.03143 / 2.14 ( 1280) hydrogen bonds : angle 3.19843 / 2.28 ( 3780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.633 Fit side-chains REVERT: A 66 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8331 (mp0) REVERT: A 172 MET cc_start: 0.9299 (mmm) cc_final: 0.8495 (mmm) REVERT: A 198 ASN cc_start: 0.8932 (m-40) cc_final: 0.8517 (m110) REVERT: B 59 MET cc_start: 0.8561 (mmt) cc_final: 0.8065 (mmt) REVERT: B 63 ASP cc_start: 0.7831 (t0) cc_final: 0.7418 (t0) REVERT: B 66 GLU cc_start: 0.8139 (mp0) cc_final: 0.7290 (mp0) REVERT: B 136 GLU cc_start: 0.8716 (tp30) cc_final: 0.8476 (tp30) REVERT: B 198 ASN cc_start: 0.8883 (m-40) cc_final: 0.8470 (m110) REVERT: B 242 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8261 (mm) REVERT: C 136 GLU cc_start: 0.8663 (tp30) cc_final: 0.8390 (tp30) REVERT: C 198 ASN cc_start: 0.8908 (m-40) cc_final: 0.8482 (m110) REVERT: D 136 GLU cc_start: 0.8757 (tp30) cc_final: 0.8476 (tp30) REVERT: D 198 ASN cc_start: 0.8818 (m-40) cc_final: 0.8443 (m110) REVERT: E 59 MET cc_start: 0.8655 (mmt) cc_final: 0.8078 (mmt) REVERT: E 136 GLU cc_start: 0.8643 (tp30) cc_final: 0.8415 (tp30) REVERT: E 198 ASN cc_start: 0.8855 (m-40) cc_final: 0.8454 (m110) REVERT: E 242 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8315 (mm) REVERT: F 66 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8326 (mp0) REVERT: F 172 MET cc_start: 0.9321 (mmm) cc_final: 0.8503 (mmm) REVERT: F 198 ASN cc_start: 0.8944 (m-40) cc_final: 0.8536 (m110) REVERT: F 242 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8342 (mm) REVERT: G 59 MET cc_start: 0.8538 (mmt) cc_final: 0.8042 (mmt) REVERT: G 136 GLU cc_start: 0.8716 (tp30) cc_final: 0.8468 (tp30) REVERT: G 198 ASN cc_start: 0.8870 (m-40) cc_final: 0.8451 (m110) REVERT: G 242 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8272 (mm) REVERT: H 136 GLU cc_start: 0.8666 (tp30) cc_final: 0.8252 (tp30) REVERT: H 198 ASN cc_start: 0.8911 (m-40) cc_final: 0.8485 (m110) REVERT: I 136 GLU cc_start: 0.8763 (tp30) cc_final: 0.8482 (tp30) REVERT: I 172 MET cc_start: 0.9307 (mmm) cc_final: 0.8452 (mmm) REVERT: I 198 ASN cc_start: 0.8791 (m-40) cc_final: 0.8418 (m110) REVERT: J 59 MET cc_start: 0.8597 (mmt) cc_final: 0.8096 (mmt) REVERT: J 136 GLU cc_start: 0.8683 (tp30) cc_final: 0.8445 (tp30) REVERT: J 198 ASN cc_start: 0.8863 (m-40) cc_final: 0.8458 (m110) REVERT: J 242 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8311 (mm) outliers start: 37 outliers final: 32 residues processed: 267 average time/residue: 0.0980 time to fit residues: 41.9474 Evaluate side-chains 292 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 217 TYR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 217 TYR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.079084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067464 restraints weight = 39620.909| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.63 r_work: 0.3012 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15700 Z= 0.142 Angle : 0.583 8.870 21230 Z= 0.281 Chirality : 0.038 0.142 2290 Planarity : 0.003 0.027 2930 Dihedral : 3.430 13.937 2280 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.74 % Allowed : 14.52 % Favored : 82.74 % 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: 3.91 (0.19), residues: 2020 helix: 3.07 (0.12), residues: 1630 sheet: None (None), residues: 0 loop : 0.35 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 247 TYR 0.012 0.001 TYR B 67 PHE 0.007 0.001 PHE C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15700) covalent geometry : angle 0.58283 / 0.28 (21230) hydrogen bonds : bond 0.03146 / 2.15 ( 1280) hydrogen bonds : angle 3.19439 / 2.28 ( 3780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3176.84 seconds wall clock time: 55 minutes 35.84 seconds (3335.84 seconds total)