Starting phenix.real_space_refine on Tue Aug 26 01:44:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9l_37374/08_2025/8w9l_37374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9l_37374/08_2025/8w9l_37374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9l_37374/08_2025/8w9l_37374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9l_37374/08_2025/8w9l_37374.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9l_37374/08_2025/8w9l_37374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9l_37374/08_2025/8w9l_37374.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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 108 5.16 5 C 20796 2.51 5 N 5568 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32616 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.64, per 1000 atoms: 0.08 Number of scatterers: 32616 At special positions: 0 Unit cell: (184.62, 174.42, 121.38, 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 108 16.00 O 6144 8.00 N 5568 7.00 C 20796 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: 1.93 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8232 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 49.2% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 51 through 64 removed outlier: 4.514A pdb=" N ILE A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 113 through 130 removed outlier: 4.278A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.175A pdb=" N ILE A 151 " --> pdb=" O TRP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 51 through 64 removed outlier: 4.514A pdb=" N ILE B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 113 through 130 removed outlier: 4.278A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE B 151 " --> pdb=" O TRP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 265 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'C' and resid 12 through 25 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 51 through 64 removed outlier: 4.513A pdb=" N ILE C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 113 through 130 removed outlier: 4.277A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE C 151 " --> pdb=" O TRP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 265 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'D' and resid 12 through 25 Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 51 through 64 removed outlier: 4.514A pdb=" N ILE D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 100 Processing helix chain 'D' and resid 105 through 109 Processing helix chain 'D' and resid 113 through 130 removed outlier: 4.278A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 removed outlier: 4.175A pdb=" N ILE D 151 " --> pdb=" O TRP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 356 through 359 Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'E' and resid 12 through 25 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 51 through 64 removed outlier: 4.513A pdb=" N ILE E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR E 81 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'E' and resid 105 through 109 Processing helix chain 'E' and resid 113 through 130 removed outlier: 4.277A pdb=" N ALA E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE E 151 " --> pdb=" O TRP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU E 197 " --> pdb=" O ILE E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 310 through 320 Processing helix chain 'E' and resid 356 through 359 Processing helix chain 'E' and resid 360 through 373 Processing helix chain 'F' and resid 12 through 25 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 51 through 64 removed outlier: 4.513A pdb=" N ILE F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR F 81 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 113 through 130 removed outlier: 4.277A pdb=" N ALA F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE F 151 " --> pdb=" O TRP F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 265 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 356 through 359 Processing helix chain 'F' and resid 360 through 373 Processing helix chain 'G' and resid 12 through 25 Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 51 through 64 removed outlier: 4.514A pdb=" N ILE G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 100 Processing helix chain 'G' and resid 105 through 109 Processing helix chain 'G' and resid 113 through 130 removed outlier: 4.278A pdb=" N ALA G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.175A pdb=" N ILE G 151 " --> pdb=" O TRP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 Processing helix chain 'G' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU G 197 " --> pdb=" O ILE G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 265 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 309 Processing helix chain 'G' and resid 310 through 320 Processing helix chain 'G' and resid 356 through 359 Processing helix chain 'G' and resid 360 through 373 Processing helix chain 'H' and resid 12 through 25 Processing helix chain 'H' and resid 36 through 41 Processing helix chain 'H' and resid 51 through 64 removed outlier: 4.514A pdb=" N ILE H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 100 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 113 through 130 removed outlier: 4.278A pdb=" N ALA H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE H 151 " --> pdb=" O TRP H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 175 Processing helix chain 'H' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU H 197 " --> pdb=" O ILE H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 265 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 309 Processing helix chain 'H' and resid 310 through 320 Processing helix chain 'H' and resid 356 through 359 Processing helix chain 'H' and resid 360 through 373 Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 36 through 41 Processing helix chain 'I' and resid 51 through 64 removed outlier: 4.513A pdb=" N ILE I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR I 81 " --> pdb=" O GLN I 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR I 82 " --> pdb=" O ASN I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 100 Processing helix chain 'I' and resid 105 through 109 Processing helix chain 'I' and resid 113 through 130 removed outlier: 4.277A pdb=" N ALA I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE I 151 " --> pdb=" O TRP I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 175 Processing helix chain 'I' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU I 197 " --> pdb=" O ILE I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 265 Processing helix chain 'I' and resid 280 through 294 Processing helix chain 'I' and resid 306 through 309 Processing helix chain 'I' and resid 310 through 320 Processing helix chain 'I' and resid 356 through 359 Processing helix chain 'I' and resid 360 through 373 Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 36 through 41 Processing helix chain 'J' and resid 51 through 64 removed outlier: 4.514A pdb=" N ILE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR J 81 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 100 Processing helix chain 'J' and resid 105 through 109 Processing helix chain 'J' and resid 113 through 130 removed outlier: 4.278A pdb=" N ALA J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 151 removed outlier: 4.175A pdb=" N ILE J 151 " --> pdb=" O TRP J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 Processing helix chain 'J' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 265 Processing helix chain 'J' and resid 280 through 294 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 320 Processing helix chain 'J' and resid 356 through 359 Processing helix chain 'J' and resid 360 through 373 Processing helix chain 'K' and resid 12 through 25 Processing helix chain 'K' and resid 36 through 41 Processing helix chain 'K' and resid 51 through 64 removed outlier: 4.513A pdb=" N ILE K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 83 removed outlier: 3.549A pdb=" N THR K 81 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 100 Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 113 through 130 removed outlier: 4.277A pdb=" N ALA K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 151 removed outlier: 4.175A pdb=" N ILE K 151 " --> pdb=" O TRP K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 265 Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 310 through 320 Processing helix chain 'K' and resid 356 through 359 Processing helix chain 'K' and resid 360 through 373 Processing helix chain 'L' and resid 12 through 25 Processing helix chain 'L' and resid 36 through 41 Processing helix chain 'L' and resid 51 through 64 removed outlier: 4.513A pdb=" N ILE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 83 removed outlier: 3.550A pdb=" N THR L 81 " --> pdb=" O GLN L 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 100 Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'L' and resid 113 through 130 removed outlier: 4.277A pdb=" N ALA L 117 " --> pdb=" O SER L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE L 151 " --> pdb=" O TRP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 175 Processing helix chain 'L' and resid 193 through 199 removed outlier: 3.515A pdb=" N GLU L 197 " --> pdb=" O ILE L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 265 Processing helix chain 'L' and resid 280 through 294 Processing helix chain 'L' and resid 306 through 309 Processing helix chain 'L' and resid 310 through 320 Processing helix chain 'L' and resid 356 through 359 Processing helix chain 'L' and resid 360 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL A 157 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP A 209 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 159 " --> pdb=" O TRP A 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 30 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE A 160 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 32 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 31 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS A 274 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 33 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA A 189 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 191 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE A 226 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA5, first strand: chain 'B' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL B 157 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP B 209 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE B 159 " --> pdb=" O TRP B 209 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 30 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE B 160 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE B 32 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA B 31 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS B 274 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 33 " --> pdb=" O CYS B 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 184 removed outlier: 3.679A pdb=" N ALA B 189 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B 191 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE B 226 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'C' and resid 179 through 180 removed outlier: 6.729A pdb=" N VAL C 157 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TRP C 209 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 159 " --> pdb=" O TRP C 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 30 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE C 160 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE C 32 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 31 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS C 274 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE C 33 " --> pdb=" O CYS C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA C 189 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 191 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE C 226 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB4, first strand: chain 'D' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL D 157 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP D 209 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 159 " --> pdb=" O TRP D 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 30 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE D 160 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 32 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA D 31 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS D 274 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE D 33 " --> pdb=" O CYS D 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'D' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA D 189 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D 191 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE D 226 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 324 through 326 Processing sheet with id=AB8, first strand: chain 'E' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL E 157 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP E 209 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE E 159 " --> pdb=" O TRP E 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE E 30 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE E 160 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE E 32 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA E 31 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS E 274 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE E 33 " --> pdb=" O CYS E 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'E' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA E 189 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE E 191 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE E 226 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 324 through 326 Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL F 157 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP F 209 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE F 159 " --> pdb=" O TRP F 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE F 30 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE F 160 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE F 32 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA F 31 " --> pdb=" O ILE F 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS F 274 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE F 33 " --> pdb=" O CYS F 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'F' and resid 183 through 184 removed outlier: 3.679A pdb=" N ALA F 189 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE F 191 " --> pdb=" O ILE F 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE F 226 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 324 through 326 Processing sheet with id=AC7, first strand: chain 'G' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL G 157 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP G 209 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE G 159 " --> pdb=" O TRP G 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE G 30 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE G 160 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE G 32 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA G 31 " --> pdb=" O ILE G 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS G 274 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE G 33 " --> pdb=" O CYS G 274 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'G' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA G 189 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE G 191 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE G 226 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 324 through 326 Processing sheet with id=AD2, first strand: chain 'H' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL H 157 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP H 209 " --> pdb=" O VAL H 157 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE H 159 " --> pdb=" O TRP H 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE H 30 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE H 160 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE H 32 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA H 31 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS H 274 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE H 33 " --> pdb=" O CYS H 274 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'H' and resid 183 through 184 removed outlier: 3.679A pdb=" N ALA H 189 " --> pdb=" O ARG H 228 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE H 191 " --> pdb=" O ILE H 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE H 226 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 324 through 326 Processing sheet with id=AD6, first strand: chain 'I' and resid 179 through 180 removed outlier: 6.729A pdb=" N VAL I 157 " --> pdb=" O LYS I 207 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TRP I 209 " --> pdb=" O VAL I 157 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE I 159 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE I 30 " --> pdb=" O GLU I 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE I 160 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE I 32 " --> pdb=" O PHE I 160 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA I 31 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS I 274 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE I 33 " --> pdb=" O CYS I 274 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'I' and resid 183 through 184 removed outlier: 3.679A pdb=" N ALA I 189 " --> pdb=" O ARG I 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE I 191 " --> pdb=" O ILE I 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE I 226 " --> pdb=" O PHE I 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 324 through 326 Processing sheet with id=AE1, first strand: chain 'J' and resid 179 through 180 removed outlier: 6.728A pdb=" N VAL J 157 " --> pdb=" O LYS J 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP J 209 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE J 159 " --> pdb=" O TRP J 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE J 30 " --> pdb=" O GLU J 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE J 160 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE J 32 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA J 31 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS J 274 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE J 33 " --> pdb=" O CYS J 274 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'J' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA J 189 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE J 191 " --> pdb=" O ILE J 226 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE J 226 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 324 through 326 Processing sheet with id=AE5, first strand: chain 'K' and resid 179 through 180 removed outlier: 6.729A pdb=" N VAL K 157 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TRP K 209 " --> pdb=" O VAL K 157 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE K 159 " --> pdb=" O TRP K 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE K 30 " --> pdb=" O GLU K 158 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE K 160 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE K 32 " --> pdb=" O PHE K 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA K 31 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS K 274 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE K 33 " --> pdb=" O CYS K 274 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AE7, first strand: chain 'K' and resid 183 through 184 removed outlier: 3.679A pdb=" N ALA K 189 " --> pdb=" O ARG K 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE K 191 " --> pdb=" O ILE K 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE K 226 " --> pdb=" O PHE K 191 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 324 through 326 Processing sheet with id=AE9, first strand: chain 'L' and resid 179 through 180 removed outlier: 6.729A pdb=" N VAL L 157 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TRP L 209 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE L 159 " --> pdb=" O TRP L 209 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE L 30 " --> pdb=" O GLU L 158 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE L 160 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE L 32 " --> pdb=" O PHE L 160 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA L 31 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS L 274 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE L 33 " --> pdb=" O CYS L 274 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'L' and resid 183 through 184 removed outlier: 3.678A pdb=" N ALA L 189 " --> pdb=" O ARG L 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE L 191 " --> pdb=" O ILE L 226 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE L 226 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 324 through 326 1501 hydrogen bonds defined for protein. 4251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10848 1.34 - 1.46: 5341 1.46 - 1.58: 16907 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 33264 Sorted by residual: bond pdb=" CG1 ILE B 95 " pdb=" CD1 ILE B 95 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE H 95 " pdb=" CD1 ILE H 95 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE K 95 " pdb=" CD1 ILE K 95 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE C 95 " pdb=" CD1 ILE C 95 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE F 95 " pdb=" CD1 ILE F 95 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 ... (remaining 33259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 44407 1.64 - 3.28: 679 3.28 - 4.92: 166 4.92 - 6.56: 0 6.56 - 8.20: 36 Bond angle restraints: 45288 Sorted by residual: angle pdb=" CA ARG H 58 " pdb=" CB ARG H 58 " pdb=" CG ARG H 58 " ideal model delta sigma weight residual 114.10 122.30 -8.20 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CA ARG B 58 " pdb=" CB ARG B 58 " pdb=" CG ARG B 58 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CA ARG J 58 " pdb=" CB ARG J 58 " pdb=" CG ARG J 58 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA ARG A 58 " pdb=" CB ARG A 58 " pdb=" CG ARG A 58 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA ARG D 58 " pdb=" CB ARG D 58 " pdb=" CG ARG D 58 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 ... (remaining 45283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 17735 13.63 - 27.26: 1741 27.26 - 40.89: 528 40.89 - 54.52: 144 54.52 - 68.15: 72 Dihedral angle restraints: 20220 sinusoidal: 7596 harmonic: 12624 Sorted by residual: dihedral pdb=" CA ILE L 193 " pdb=" C ILE L 193 " pdb=" N ARG L 194 " pdb=" CA ARG L 194 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE I 193 " pdb=" C ILE I 193 " pdb=" N ARG I 194 " pdb=" CA ARG I 194 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE F 193 " pdb=" C ILE F 193 " pdb=" N ARG F 194 " pdb=" CA ARG F 194 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 20217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3583 0.036 - 0.071: 1231 0.071 - 0.107: 327 0.107 - 0.143: 139 0.143 - 0.179: 12 Chirality restraints: 5292 Sorted by residual: chirality pdb=" CA ARG C 58 " pdb=" N ARG C 58 " pdb=" C ARG C 58 " pdb=" CB ARG C 58 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ARG F 58 " pdb=" N ARG F 58 " pdb=" C ARG F 58 " pdb=" CB ARG F 58 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ARG L 58 " pdb=" N ARG L 58 " pdb=" C ARG L 58 " pdb=" CB ARG L 58 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 5289 not shown) Planarity restraints: 5868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 239 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO C 240 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 239 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO F 240 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 240 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 240 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 239 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 240 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " 0.025 5.00e-02 4.00e+02 ... (remaining 5865 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5443 2.77 - 3.30: 31458 3.30 - 3.83: 52413 3.83 - 4.37: 59260 4.37 - 4.90: 103835 Nonbonded interactions: 252409 Sorted by model distance: nonbonded pdb=" O ASN C 78 " pdb=" OG1 THR C 81 " model vdw 2.232 3.040 nonbonded pdb=" O ASN L 78 " pdb=" OG1 THR L 81 " model vdw 2.232 3.040 nonbonded pdb=" O ASN I 78 " pdb=" OG1 THR I 81 " model vdw 2.233 3.040 nonbonded pdb=" O ASN K 78 " pdb=" OG1 THR K 81 " model vdw 2.233 3.040 nonbonded pdb=" O ASN B 78 " pdb=" OG1 THR B 81 " model vdw 2.233 3.040 ... (remaining 252404 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: 0.13 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' selection = chain 'K' selection = chain 'L' } 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.640 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 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 : 0.002 0.046 33264 Z= 0.110 Angle : 0.552 8.196 45288 Z= 0.293 Chirality : 0.042 0.179 5292 Planarity : 0.005 0.058 5868 Dihedral : 13.511 68.152 11988 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.48 (0.14), residues: 4272 helix: 1.92 (0.13), residues: 1872 sheet: -0.66 (0.22), residues: 552 loop : -1.06 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 58 TYR 0.006 0.001 TYR H 164 PHE 0.009 0.001 PHE I 263 TRP 0.007 0.001 TRP E 147 HIS 0.003 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00245 (33264) covalent geometry : angle 0.55162 (45288) hydrogen bonds : bond 0.17432 ( 1501) hydrogen bonds : angle 5.76890 ( 4251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.2241 time to fit residues: 176.9964 Evaluate side-chains 341 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN D 292 GLN G 292 GLN J 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.223894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175589 restraints weight = 40306.394| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.92 r_work: 0.3976 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33264 Z= 0.131 Angle : 0.521 6.398 45288 Z= 0.266 Chirality : 0.043 0.145 5292 Planarity : 0.005 0.058 5868 Dihedral : 3.942 15.939 4512 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.46 % Allowed : 6.16 % Favored : 92.38 % 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 aren not related in a simple way. whole: 0.29 (0.14), residues: 4272 helix: 1.88 (0.12), residues: 1932 sheet: -1.07 (0.21), residues: 552 loop : -1.31 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 58 TYR 0.011 0.001 TYR E 179 PHE 0.015 0.002 PHE H 367 TRP 0.024 0.002 TRP B 147 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00299 (33264) covalent geometry : angle 0.52101 (45288) hydrogen bonds : bond 0.03687 ( 1501) hydrogen bonds : angle 4.55112 ( 4251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 1.074 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: A 73 MET cc_start: 0.8820 (mmm) cc_final: 0.8395 (tpp) REVERT: B 32 PHE cc_start: 0.8050 (m-80) cc_final: 0.7770 (m-80) REVERT: B 155 HIS cc_start: 0.7098 (m170) cc_final: 0.6895 (m170) REVERT: C 40 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7275 (p) REVERT: C 155 HIS cc_start: 0.7016 (m170) cc_final: 0.6776 (m170) REVERT: C 292 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6191 (pt0) REVERT: D 73 MET cc_start: 0.8821 (mmm) cc_final: 0.8396 (tpp) REVERT: E 32 PHE cc_start: 0.8060 (m-80) cc_final: 0.7772 (m-80) REVERT: E 155 HIS cc_start: 0.6996 (m170) cc_final: 0.6782 (m170) REVERT: F 40 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7314 (p) REVERT: F 155 HIS cc_start: 0.6820 (m170) cc_final: 0.6597 (m-70) REVERT: F 292 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6299 (pt0) REVERT: G 73 MET cc_start: 0.8817 (mmm) cc_final: 0.8391 (tpp) REVERT: H 32 PHE cc_start: 0.7994 (m-80) cc_final: 0.7700 (m-80) REVERT: H 155 HIS cc_start: 0.7005 (m170) cc_final: 0.6792 (m170) REVERT: I 40 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7312 (p) REVERT: I 155 HIS cc_start: 0.7003 (m170) cc_final: 0.6774 (m170) REVERT: I 292 GLN cc_start: 0.6527 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: J 73 MET cc_start: 0.8818 (mmm) cc_final: 0.8394 (tpp) REVERT: L 40 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7275 (p) REVERT: L 155 HIS cc_start: 0.6877 (m170) cc_final: 0.6617 (m-70) REVERT: L 292 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6274 (pt0) outliers start: 49 outliers final: 15 residues processed: 438 average time/residue: 0.2060 time to fit residues: 138.9780 Evaluate side-chains 399 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 376 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 292 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 373 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 298 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 198 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 364 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN D 218 GLN G 218 GLN H 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.225501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.179620 restraints weight = 40117.177| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.70 r_work: 0.3982 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33264 Z= 0.098 Angle : 0.472 6.309 45288 Z= 0.237 Chirality : 0.041 0.134 5292 Planarity : 0.004 0.042 5868 Dihedral : 3.720 16.164 4512 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.95 % Allowed : 9.67 % Favored : 89.38 % 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 aren not related in a simple way. whole: 0.42 (0.14), residues: 4272 helix: 1.98 (0.12), residues: 1932 sheet: -1.15 (0.21), residues: 552 loop : -1.17 (0.16), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 58 TYR 0.007 0.001 TYR L 179 PHE 0.023 0.002 PHE K 367 TRP 0.022 0.001 TRP E 147 HIS 0.002 0.000 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00223 (33264) covalent geometry : angle 0.47153 (45288) hydrogen bonds : bond 0.03067 ( 1501) hydrogen bonds : angle 4.26745 ( 4251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 413 time to evaluate : 1.456 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7118 (p) REVERT: A 73 MET cc_start: 0.8781 (mmm) cc_final: 0.8400 (tpp) REVERT: A 316 MET cc_start: 0.6192 (tpt) cc_final: 0.5979 (tpt) REVERT: C 40 VAL cc_start: 0.7568 (p) cc_final: 0.7311 (p) REVERT: C 58 ARG cc_start: 0.8415 (ptp90) cc_final: 0.8185 (ptp90) REVERT: C 155 HIS cc_start: 0.7019 (m170) cc_final: 0.6772 (m170) REVERT: D 40 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7114 (p) REVERT: D 73 MET cc_start: 0.8785 (mmm) cc_final: 0.8405 (tpp) REVERT: D 316 MET cc_start: 0.6192 (tpt) cc_final: 0.5978 (tpt) REVERT: E 155 HIS cc_start: 0.7043 (m170) cc_final: 0.6837 (m170) REVERT: F 40 VAL cc_start: 0.7569 (p) cc_final: 0.7307 (p) REVERT: F 155 HIS cc_start: 0.7002 (m170) cc_final: 0.6791 (m-70) REVERT: G 40 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7119 (p) REVERT: G 73 MET cc_start: 0.8783 (mmm) cc_final: 0.8402 (tpp) REVERT: G 316 MET cc_start: 0.6195 (tpt) cc_final: 0.5964 (tpt) REVERT: H 155 HIS cc_start: 0.7047 (m170) cc_final: 0.6840 (m170) REVERT: I 40 VAL cc_start: 0.7575 (p) cc_final: 0.7308 (p) REVERT: I 58 ARG cc_start: 0.8400 (ptp90) cc_final: 0.8186 (ptp90) REVERT: I 155 HIS cc_start: 0.7077 (m170) cc_final: 0.6840 (m170) REVERT: J 40 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7101 (p) REVERT: J 73 MET cc_start: 0.8783 (mmm) cc_final: 0.8402 (tpp) REVERT: J 316 MET cc_start: 0.6181 (tpt) cc_final: 0.5957 (tpt) REVERT: L 40 VAL cc_start: 0.7543 (p) cc_final: 0.7278 (p) REVERT: L 155 HIS cc_start: 0.6974 (m170) cc_final: 0.6755 (m-70) outliers start: 32 outliers final: 11 residues processed: 433 average time/residue: 0.2236 time to fit residues: 148.0843 Evaluate side-chains 388 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 373 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 292 GLN Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 327 optimal weight: 6.9990 chunk 423 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 33 optimal weight: 50.0000 chunk 337 optimal weight: 4.9990 chunk 321 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS C 218 GLN C 239 HIS E 218 GLN E 239 HIS F 239 HIS G 292 GLN H 239 HIS I 218 GLN I 239 HIS J 218 GLN J 292 GLN K 218 GLN K 239 HIS L 239 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.216457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.169378 restraints weight = 39845.203| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.93 r_work: 0.3893 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33264 Z= 0.228 Angle : 0.604 6.808 45288 Z= 0.307 Chirality : 0.046 0.162 5292 Planarity : 0.005 0.042 5868 Dihedral : 4.527 24.397 4512 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.08 % Allowed : 10.71 % Favored : 87.20 % 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 aren not related in a simple way. whole: -0.01 (0.14), residues: 4272 helix: 1.68 (0.12), residues: 1920 sheet: -1.69 (0.21), residues: 552 loop : -1.33 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 204 TYR 0.015 0.002 TYR I 179 PHE 0.014 0.003 PHE H 367 TRP 0.020 0.002 TRP B 147 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00544 (33264) covalent geometry : angle 0.60367 (45288) hydrogen bonds : bond 0.03847 ( 1501) hydrogen bonds : angle 4.57608 ( 4251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 378 time to evaluate : 1.285 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.6264 (mt0) cc_final: 0.6052 (mt0) REVERT: D 156 GLN cc_start: 0.6254 (mt0) cc_final: 0.6048 (mt0) REVERT: G 156 GLN cc_start: 0.6270 (mt0) cc_final: 0.6062 (mt0) REVERT: G 292 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6639 (pt0) REVERT: J 156 GLN cc_start: 0.6259 (mt0) cc_final: 0.6049 (mt0) REVERT: J 292 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6641 (pt0) outliers start: 70 outliers final: 34 residues processed: 426 average time/residue: 0.2200 time to fit residues: 143.6550 Evaluate side-chains 365 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 292 GLN Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 GLN Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 337 optimal weight: 0.6980 chunk 405 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 203 optimal weight: 0.4980 chunk 324 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN D 15 GLN F 218 GLN G 15 GLN G 292 GLN J 15 GLN J 292 GLN L 218 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.221647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.177334 restraints weight = 39950.971| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.66 r_work: 0.3979 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33264 Z= 0.103 Angle : 0.511 7.275 45288 Z= 0.251 Chirality : 0.042 0.167 5292 Planarity : 0.004 0.042 5868 Dihedral : 3.937 18.243 4512 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.76 % Allowed : 12.71 % Favored : 85.54 % 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 aren not related in a simple way. whole: 0.30 (0.14), residues: 4272 helix: 1.97 (0.12), residues: 1920 sheet: -1.58 (0.21), residues: 552 loop : -1.19 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 58 TYR 0.007 0.001 TYR A 253 PHE 0.025 0.001 PHE H 367 TRP 0.029 0.002 TRP G 147 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00237 (33264) covalent geometry : angle 0.51084 (45288) hydrogen bonds : bond 0.02862 ( 1501) hydrogen bonds : angle 4.27421 ( 4251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 370 time to evaluate : 0.968 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: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.7024 (p) REVERT: C 40 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7416 (p) REVERT: C 292 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: D 40 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7068 (p) REVERT: F 292 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6542 (pt0) REVERT: G 40 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7060 (p) REVERT: G 292 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6884 (pt0) REVERT: I 40 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7423 (p) REVERT: I 292 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6539 (pt0) REVERT: J 40 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7056 (p) REVERT: J 292 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: L 40 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7477 (p) outliers start: 59 outliers final: 23 residues processed: 409 average time/residue: 0.2203 time to fit residues: 136.3577 Evaluate side-chains 370 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 335 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 292 GLN Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 GLN Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 20 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 358 optimal weight: 0.9990 chunk 405 optimal weight: 2.9990 chunk 431 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN C 44 HIS E 15 GLN F 44 HIS G 292 GLN H 15 GLN I 44 HIS J 292 GLN K 15 GLN L 44 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.220102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.171845 restraints weight = 40018.638| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.06 r_work: 0.3924 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33264 Z= 0.135 Angle : 0.541 8.794 45288 Z= 0.268 Chirality : 0.043 0.166 5292 Planarity : 0.004 0.041 5868 Dihedral : 4.042 19.539 4512 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.64 % Allowed : 13.63 % Favored : 84.73 % 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 aren not related in a simple way. whole: 0.31 (0.14), residues: 4272 helix: 1.97 (0.12), residues: 1932 sheet: -1.56 (0.21), residues: 552 loop : -1.20 (0.16), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 58 TYR 0.010 0.001 TYR I 179 PHE 0.025 0.002 PHE H 367 TRP 0.028 0.002 TRP H 147 HIS 0.002 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00321 (33264) covalent geometry : angle 0.54149 (45288) hydrogen bonds : bond 0.03032 ( 1501) hydrogen bonds : angle 4.32741 ( 4251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 351 time to evaluate : 1.263 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 21 HIS cc_start: 0.7182 (m90) cc_final: 0.6838 (m90) REVERT: A 40 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.6995 (p) REVERT: A 73 MET cc_start: 0.8948 (mmm) cc_final: 0.8744 (mmm) REVERT: A 164 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: C 155 HIS cc_start: 0.7237 (m170) cc_final: 0.6984 (m170) REVERT: D 40 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.7009 (p) REVERT: D 73 MET cc_start: 0.8943 (mmm) cc_final: 0.8740 (mmm) REVERT: D 164 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: F 40 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7420 (p) REVERT: G 40 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.6991 (p) REVERT: G 80 LYS cc_start: 0.7594 (mmtt) cc_final: 0.6977 (mmtt) REVERT: G 164 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: G 292 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6638 (pt0) REVERT: I 155 HIS cc_start: 0.7242 (m170) cc_final: 0.6992 (m170) REVERT: J 40 VAL cc_start: 0.7304 (OUTLIER) cc_final: 0.6997 (p) REVERT: J 80 LYS cc_start: 0.7600 (mmtt) cc_final: 0.6985 (mmtt) REVERT: J 164 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: J 292 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: L 40 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7306 (p) outliers start: 55 outliers final: 18 residues processed: 385 average time/residue: 0.2341 time to fit residues: 134.9606 Evaluate side-chains 356 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 326 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 292 GLN Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 164 TYR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 GLN Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 109 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 299 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 412 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 403 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 292 GLN J 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.221728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.177121 restraints weight = 40141.361| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.80 r_work: 0.3950 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33264 Z= 0.108 Angle : 0.533 10.378 45288 Z= 0.259 Chirality : 0.042 0.172 5292 Planarity : 0.004 0.041 5868 Dihedral : 3.873 19.079 4512 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.64 % Allowed : 14.97 % Favored : 83.39 % 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 aren not related in a simple way. whole: 0.40 (0.14), residues: 4272 helix: 2.12 (0.12), residues: 1860 sheet: -1.50 (0.22), residues: 552 loop : -1.12 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 58 TYR 0.008 0.001 TYR D 253 PHE 0.024 0.001 PHE E 367 TRP 0.035 0.002 TRP E 147 HIS 0.002 0.000 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00257 (33264) covalent geometry : angle 0.53275 (45288) hydrogen bonds : bond 0.02783 ( 1501) hydrogen bonds : angle 4.24019 ( 4251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 368 time to evaluate : 1.296 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 HIS cc_start: 0.7145 (m90) cc_final: 0.6814 (m90) REVERT: A 40 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.6916 (p) REVERT: D 40 VAL cc_start: 0.7273 (OUTLIER) cc_final: 0.6908 (p) REVERT: F 40 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7325 (p) REVERT: G 40 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.6900 (p) REVERT: G 292 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6372 (pt0) REVERT: I 155 HIS cc_start: 0.7270 (m170) cc_final: 0.7036 (m170) REVERT: J 40 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6897 (p) REVERT: J 292 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6370 (pt0) outliers start: 55 outliers final: 34 residues processed: 407 average time/residue: 0.2543 time to fit residues: 155.4598 Evaluate side-chains 381 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 292 GLN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 GLN Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 191 optimal weight: 0.9980 chunk 281 optimal weight: 0.0670 chunk 209 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 321 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 367 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 264 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS C 199 ASN G 292 GLN J 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.222746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178341 restraints weight = 40029.797| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.68 r_work: 0.3969 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33264 Z= 0.102 Angle : 0.537 11.079 45288 Z= 0.260 Chirality : 0.042 0.175 5292 Planarity : 0.004 0.042 5868 Dihedral : 3.776 20.084 4512 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.52 % Allowed : 15.27 % Favored : 83.21 % 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 aren not related in a simple way. whole: 0.47 (0.14), residues: 4272 helix: 2.17 (0.12), residues: 1860 sheet: -1.45 (0.22), residues: 552 loop : -1.07 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 58 TYR 0.008 0.001 TYR A 253 PHE 0.022 0.001 PHE B 367 TRP 0.032 0.002 TRP E 147 HIS 0.002 0.000 HIS L 142 Details of bonding type rmsd covalent geometry : bond 0.00241 (33264) covalent geometry : angle 0.53662 (45288) hydrogen bonds : bond 0.02707 ( 1501) hydrogen bonds : angle 4.21730 ( 4251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 381 time to evaluate : 1.232 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: symmetry clash revert: symmetry clash REVERT: A 21 HIS cc_start: 0.7138 (m90) cc_final: 0.6819 (m90) REVERT: A 40 VAL cc_start: 0.7511 (p) cc_final: 0.7199 (p) REVERT: A 94 TYR cc_start: 0.7888 (t80) cc_final: 0.7641 (t80) REVERT: A 200 LYS cc_start: 0.7919 (ptpp) cc_final: 0.7596 (ptmm) REVERT: B 58 ARG cc_start: 0.8425 (ptp90) cc_final: 0.8058 (ptp90) REVERT: C 292 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6418 (pt0) REVERT: D 40 VAL cc_start: 0.7492 (p) cc_final: 0.7181 (p) REVERT: D 94 TYR cc_start: 0.7883 (t80) cc_final: 0.7636 (t80) REVERT: D 200 LYS cc_start: 0.7966 (ptpp) cc_final: 0.7615 (ptmm) REVERT: E 58 ARG cc_start: 0.8438 (ptp90) cc_final: 0.8069 (ptp90) REVERT: E 155 HIS cc_start: 0.7145 (m170) cc_final: 0.6927 (m170) REVERT: G 40 VAL cc_start: 0.7501 (p) cc_final: 0.7187 (p) REVERT: G 94 TYR cc_start: 0.7853 (t80) cc_final: 0.7631 (t80) REVERT: G 200 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7617 (ptmm) REVERT: G 292 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6335 (pt0) REVERT: H 58 ARG cc_start: 0.8417 (ptp90) cc_final: 0.8052 (ptp90) REVERT: H 155 HIS cc_start: 0.7124 (m170) cc_final: 0.6906 (m170) REVERT: J 40 VAL cc_start: 0.7494 (p) cc_final: 0.7182 (p) REVERT: J 94 TYR cc_start: 0.7852 (t80) cc_final: 0.7629 (t80) REVERT: J 200 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7625 (ptmm) REVERT: J 292 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6329 (pt0) REVERT: K 58 ARG cc_start: 0.8450 (ptp90) cc_final: 0.8077 (ptp90) REVERT: L 292 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6433 (pt0) outliers start: 51 outliers final: 29 residues processed: 417 average time/residue: 0.2269 time to fit residues: 142.5258 Evaluate side-chains 383 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 350 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 292 GLN Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 292 GLN Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 273 THR Chi-restraints excluded: chain L residue 292 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 342 optimal weight: 0.9990 chunk 337 optimal weight: 1.9990 chunk 364 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS D 44 HIS E 44 HIS G 44 HIS G 292 GLN H 44 HIS J 44 HIS J 292 GLN K 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.219971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.169237 restraints weight = 39528.340| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.14 r_work: 0.3905 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33264 Z= 0.133 Angle : 0.570 11.397 45288 Z= 0.280 Chirality : 0.043 0.172 5292 Planarity : 0.004 0.040 5868 Dihedral : 3.965 22.925 4512 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.34 % Allowed : 16.04 % Favored : 82.62 % 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 aren not related in a simple way. whole: 0.41 (0.14), residues: 4272 helix: 2.05 (0.12), residues: 1932 sheet: -1.49 (0.22), residues: 552 loop : -1.15 (0.16), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 194 TYR 0.009 0.001 TYR I 179 PHE 0.026 0.002 PHE B 367 TRP 0.036 0.002 TRP K 147 HIS 0.002 0.000 HIS J 142 Details of bonding type rmsd covalent geometry : bond 0.00321 (33264) covalent geometry : angle 0.56980 (45288) hydrogen bonds : bond 0.02954 ( 1501) hydrogen bonds : angle 4.25671 ( 4251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 361 time to evaluate : 1.283 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: symmetry clash revert: symmetry clash REVERT: A 21 HIS cc_start: 0.7171 (m90) cc_final: 0.6834 (m90) REVERT: A 58 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8352 (ptp90) REVERT: A 200 LYS cc_start: 0.8059 (ptpp) cc_final: 0.7652 (ptmm) REVERT: B 40 VAL cc_start: 0.7358 (p) cc_final: 0.7012 (p) REVERT: B 58 ARG cc_start: 0.8520 (ptp90) cc_final: 0.8102 (ptp90) REVERT: C 58 ARG cc_start: 0.8792 (ptp90) cc_final: 0.8535 (ptp90) REVERT: D 21 HIS cc_start: 0.7116 (m90) cc_final: 0.6782 (m90) REVERT: D 58 ARG cc_start: 0.8592 (ptp90) cc_final: 0.8365 (ptp90) REVERT: D 200 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7665 (ptmm) REVERT: E 40 VAL cc_start: 0.7334 (p) cc_final: 0.6986 (p) REVERT: E 58 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8088 (ptp90) REVERT: E 155 HIS cc_start: 0.7259 (m170) cc_final: 0.7019 (m170) REVERT: G 21 HIS cc_start: 0.7113 (m90) cc_final: 0.6781 (m90) REVERT: G 58 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8350 (ptp90) REVERT: G 200 LYS cc_start: 0.8051 (ptpp) cc_final: 0.7660 (ptmm) REVERT: H 40 VAL cc_start: 0.7345 (p) cc_final: 0.6998 (p) REVERT: H 58 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8074 (ptp90) REVERT: H 155 HIS cc_start: 0.7247 (m170) cc_final: 0.7009 (m170) REVERT: I 58 ARG cc_start: 0.8813 (ptp90) cc_final: 0.8548 (ptp90) REVERT: J 21 HIS cc_start: 0.7095 (m90) cc_final: 0.6768 (m90) REVERT: J 58 ARG cc_start: 0.8583 (ptp90) cc_final: 0.8358 (ptp90) REVERT: J 200 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7660 (ptmm) REVERT: K 40 VAL cc_start: 0.7329 (p) cc_final: 0.6981 (p) REVERT: K 58 ARG cc_start: 0.8518 (ptp90) cc_final: 0.8094 (ptp90) outliers start: 45 outliers final: 26 residues processed: 402 average time/residue: 0.2176 time to fit residues: 131.8168 Evaluate side-chains 372 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 346 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 260 optimal weight: 2.9990 chunk 395 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 378 optimal weight: 0.9990 chunk 327 optimal weight: 0.0040 chunk 168 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 333 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 401 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN I 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.222929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.179371 restraints weight = 39894.382| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.69 r_work: 0.3983 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33264 Z= 0.105 Angle : 0.561 12.203 45288 Z= 0.276 Chirality : 0.043 0.195 5292 Planarity : 0.004 0.042 5868 Dihedral : 3.722 20.100 4512 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.83 % Allowed : 16.49 % 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 aren not related in a simple way. whole: 0.50 (0.14), residues: 4272 helix: 2.18 (0.12), residues: 1860 sheet: -1.37 (0.22), residues: 552 loop : -1.06 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 58 TYR 0.010 0.001 TYR K 253 PHE 0.027 0.001 PHE H 367 TRP 0.041 0.002 TRP E 147 HIS 0.002 0.000 HIS L 142 Details of bonding type rmsd covalent geometry : bond 0.00251 (33264) covalent geometry : angle 0.56110 (45288) hydrogen bonds : bond 0.02684 ( 1501) hydrogen bonds : angle 4.26126 ( 4251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 370 time to evaluate : 1.315 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: symmetry clash revert: symmetry clash REVERT: A 21 HIS cc_start: 0.7144 (m90) cc_final: 0.6860 (m90) REVERT: A 200 LYS cc_start: 0.7880 (ptpp) cc_final: 0.7629 (ptmm) REVERT: B 21 HIS cc_start: 0.7067 (m90) cc_final: 0.6782 (m90) REVERT: B 40 VAL cc_start: 0.7458 (p) cc_final: 0.7100 (p) REVERT: B 43 ARG cc_start: 0.7774 (mmt-90) cc_final: 0.7298 (mmp80) REVERT: B 58 ARG cc_start: 0.8459 (ptp90) cc_final: 0.8120 (ptp90) REVERT: C 43 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7273 (mmp-170) REVERT: C 58 ARG cc_start: 0.8685 (ptp90) cc_final: 0.8428 (ptp90) REVERT: D 21 HIS cc_start: 0.7056 (m90) cc_final: 0.6765 (m90) REVERT: D 200 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7616 (ptmm) REVERT: E 21 HIS cc_start: 0.7052 (m90) cc_final: 0.6770 (m90) REVERT: E 40 VAL cc_start: 0.7429 (p) cc_final: 0.7070 (p) REVERT: E 43 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7296 (mmp80) REVERT: E 58 ARG cc_start: 0.8473 (ptp90) cc_final: 0.8102 (ptp90) REVERT: E 155 HIS cc_start: 0.7095 (m170) cc_final: 0.6888 (m170) REVERT: F 43 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7257 (mmp-170) REVERT: F 58 ARG cc_start: 0.8740 (ptp90) cc_final: 0.8498 (ptp90) REVERT: G 21 HIS cc_start: 0.7051 (m90) cc_final: 0.6758 (m90) REVERT: G 200 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7621 (ptmm) REVERT: H 21 HIS cc_start: 0.7061 (m90) cc_final: 0.6778 (m90) REVERT: H 40 VAL cc_start: 0.7459 (p) cc_final: 0.7099 (p) REVERT: H 43 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7267 (mmp80) REVERT: H 58 ARG cc_start: 0.8438 (ptp90) cc_final: 0.8074 (ptp90) REVERT: I 43 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7254 (mmp-170) REVERT: I 58 ARG cc_start: 0.8716 (ptp90) cc_final: 0.8443 (ptp90) REVERT: J 21 HIS cc_start: 0.7053 (m90) cc_final: 0.6761 (m90) REVERT: J 200 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7625 (ptmm) REVERT: K 40 VAL cc_start: 0.7431 (p) cc_final: 0.7069 (p) REVERT: K 43 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7274 (mmp80) REVERT: K 58 ARG cc_start: 0.8468 (ptp90) cc_final: 0.8125 (ptp90) REVERT: L 43 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7267 (mmp-170) REVERT: L 58 ARG cc_start: 0.8728 (ptp90) cc_final: 0.8464 (ptp90) outliers start: 28 outliers final: 27 residues processed: 395 average time/residue: 0.2465 time to fit residues: 144.9845 Evaluate side-chains 381 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 261 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 201 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 375 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 379 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN D 14 GLN E 14 GLN G 14 GLN H 14 GLN J 14 GLN K 14 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.223200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.170511 restraints weight = 40193.300| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.98 r_work: 0.3934 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33264 Z= 0.107 Angle : 0.564 12.339 45288 Z= 0.273 Chirality : 0.043 0.184 5292 Planarity : 0.005 0.055 5868 Dihedral : 3.701 19.654 4512 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.13 % Allowed : 16.58 % Favored : 82.29 % 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 aren not related in a simple way. whole: 0.53 (0.14), residues: 4272 helix: 2.23 (0.12), residues: 1860 sheet: -1.32 (0.22), residues: 552 loop : -1.08 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 194 TYR 0.009 0.001 TYR K 253 PHE 0.028 0.001 PHE E 367 TRP 0.037 0.002 TRP H 147 HIS 0.002 0.000 HIS I 142 Details of bonding type rmsd covalent geometry : bond 0.00257 (33264) covalent geometry : angle 0.56353 (45288) hydrogen bonds : bond 0.02650 ( 1501) hydrogen bonds : angle 4.26679 ( 4251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7870.23 seconds wall clock time: 135 minutes 35.47 seconds (8135.47 seconds total)