Starting phenix.real_space_refine on Thu May 29 18:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9l_37374/05_2025/8w9l_37374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9l_37374/05_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_37374/05_2025/8w9l_37374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9l_37374/05_2025/8w9l_37374.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9l_37374/05_2025/8w9l_37374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9l_37374/05_2025/8w9l_37374.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 112 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 9.34, per 1000 atoms: 0.29 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: 8.43 Conformation dependent library (CDL) restraints added in 4.5 seconds 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: 4.70 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: 11.68 Time building geometry restraints manager: 9.69 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: 0.31 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 61.630 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (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 TRP 0.007 0.001 TRP E 147 HIS 0.003 0.001 HIS H 155 PHE 0.009 0.001 PHE I 263 TYR 0.006 0.001 TYR H 164 ARG 0.013 0.001 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.17432 ( 1501) hydrogen bonds : angle 5.76890 ( 4251) covalent geometry : bond 0.00245 (33264) covalent geometry : angle 0.55162 (45288) *********************** 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 : 3.367 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: 0.5076 time to fit residues: 397.7119 Evaluate side-chains 329 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 181 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 338 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 0.1980 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN B 239 HIS C 239 HIS D 292 GLN E 239 HIS F 239 HIS G 292 GLN H 239 HIS I 239 HIS J 292 GLN K 239 HIS L 239 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.217717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.169510 restraints weight = 40292.743| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.74 r_work: 0.3912 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 33264 Z= 0.246 Angle : 0.643 5.479 45288 Z= 0.335 Chirality : 0.048 0.171 5292 Planarity : 0.006 0.066 5868 Dihedral : 4.636 23.296 4512 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.82 % Allowed : 7.38 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4272 helix: 1.54 (0.12), residues: 1932 sheet: -1.69 (0.21), residues: 552 loop : -1.53 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 147 HIS 0.003 0.001 HIS A 282 PHE 0.014 0.003 PHE K 64 TYR 0.019 0.003 TYR I 179 ARG 0.010 0.001 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 1501) hydrogen bonds : angle 4.76889 ( 4251) covalent geometry : bond 0.00585 (33264) covalent geometry : angle 0.64285 (45288) *********************** 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 452 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 391 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8815 (mmm) cc_final: 0.8447 (tpp) REVERT: C 155 HIS cc_start: 0.7069 (m170) cc_final: 0.6852 (m170) REVERT: D 58 ARG cc_start: 0.8362 (ptp90) cc_final: 0.8162 (ptp90) REVERT: D 73 MET cc_start: 0.8815 (mmm) cc_final: 0.8450 (tpp) REVERT: G 73 MET cc_start: 0.8811 (mmm) cc_final: 0.8443 (tpp) REVERT: I 155 HIS cc_start: 0.7087 (m170) cc_final: 0.6882 (m170) REVERT: J 73 MET cc_start: 0.8812 (mmm) cc_final: 0.8444 (tpp) REVERT: L 155 HIS cc_start: 0.6911 (m170) cc_final: 0.6708 (m-70) outliers start: 61 outliers final: 18 residues processed: 431 average time/residue: 0.4931 time to fit residues: 323.3917 Evaluate side-chains 376 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 358 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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 D residue 151 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain G residue 151 ILE 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 J residue 151 ILE Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 348 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 418 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 416 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 218 GLN B 218 GLN C 218 GLN D 15 GLN D 218 GLN F 218 GLN G 15 GLN G 218 GLN H 218 GLN I 218 GLN J 15 GLN J 218 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.220792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.172654 restraints weight = 40141.712| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.67 r_work: 0.3922 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33264 Z= 0.132 Angle : 0.521 6.518 45288 Z= 0.268 Chirality : 0.043 0.144 5292 Planarity : 0.005 0.054 5868 Dihedral : 4.187 19.610 4512 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.08 % Allowed : 10.21 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 4272 helix: 1.75 (0.12), residues: 1920 sheet: -1.68 (0.21), residues: 552 loop : -1.40 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 147 HIS 0.002 0.001 HIS B 142 PHE 0.022 0.002 PHE E 367 TYR 0.009 0.001 TYR F 179 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 1501) hydrogen bonds : angle 4.44135 ( 4251) covalent geometry : bond 0.00308 (33264) covalent geometry : angle 0.52146 (45288) *********************** 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 467 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 397 time to evaluate : 4.323 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 40 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7183 (p) REVERT: A 155 HIS cc_start: 0.6988 (m170) cc_final: 0.6784 (m-70) REVERT: B 15 GLN cc_start: 0.5351 (mp10) cc_final: 0.4740 (mp10) REVERT: B 164 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: C 40 VAL cc_start: 0.7537 (p) cc_final: 0.7317 (p) REVERT: C 155 HIS cc_start: 0.7147 (m170) cc_final: 0.6937 (m170) REVERT: C 292 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: D 40 VAL cc_start: 0.7474 (OUTLIER) cc_final: 0.7174 (p) REVERT: D 155 HIS cc_start: 0.6990 (m170) cc_final: 0.6784 (m-70) REVERT: E 15 GLN cc_start: 0.5351 (mp10) cc_final: 0.4747 (mp10) REVERT: E 164 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: F 40 VAL cc_start: 0.7539 (p) cc_final: 0.7321 (p) REVERT: F 292 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6587 (pt0) REVERT: G 40 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7169 (p) REVERT: G 155 HIS cc_start: 0.6998 (m170) cc_final: 0.6790 (m-70) REVERT: H 15 GLN cc_start: 0.5348 (mp10) cc_final: 0.4725 (mp10) REVERT: H 164 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: I 292 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6570 (pt0) REVERT: J 40 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7169 (p) REVERT: J 155 HIS cc_start: 0.6978 (m170) cc_final: 0.6770 (m-70) REVERT: K 15 GLN cc_start: 0.5343 (mp10) cc_final: 0.4740 (mp10) REVERT: K 164 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: L 40 VAL cc_start: 0.7540 (p) cc_final: 0.7324 (p) REVERT: L 292 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6586 (pt0) outliers start: 70 outliers final: 30 residues processed: 437 average time/residue: 0.5023 time to fit residues: 333.1725 Evaluate side-chains 401 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 LYS 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 B residue 151 ILE Chi-restraints excluded: chain B residue 164 TYR 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 C residue 292 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 80 LYS 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 E residue 151 ILE Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 273 THR 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 80 LYS 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 H residue 151 ILE Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H 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 80 LYS 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 K residue 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 273 THR Chi-restraints excluded: chain L residue 292 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 45 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 364 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 402 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 296 ASN B 44 HIS B 296 ASN C 44 HIS C 296 ASN D 239 HIS D 296 ASN E 44 HIS E 218 GLN E 296 ASN F 44 HIS F 296 ASN G 239 HIS G 296 ASN H 44 HIS H 296 ASN I 44 HIS I 296 ASN J 239 HIS J 296 ASN K 44 HIS K 218 GLN K 296 ASN L 44 HIS L 296 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.213439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.165637 restraints weight = 40369.462| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.77 r_work: 0.3829 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 33264 Z= 0.308 Angle : 0.713 6.782 45288 Z= 0.370 Chirality : 0.049 0.173 5292 Planarity : 0.006 0.053 5868 Dihedral : 5.269 27.374 4512 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.77 % Allowed : 13.90 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4272 helix: 1.29 (0.12), residues: 1848 sheet: -2.26 (0.21), residues: 552 loop : -1.65 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 147 HIS 0.005 0.001 HIS H 363 PHE 0.021 0.003 PHE H 367 TYR 0.020 0.003 TYR H 179 ARG 0.003 0.001 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 1501) hydrogen bonds : angle 4.97648 ( 4251) covalent geometry : bond 0.00727 (33264) covalent geometry : angle 0.71269 (45288) *********************** 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 464 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 371 time to evaluate : 3.679 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: 0.7194 (m90) cc_final: 0.6808 (m-70) REVERT: A 164 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: A 283 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8165 (mt) REVERT: B 164 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: C 58 ARG cc_start: 0.8694 (ptp90) cc_final: 0.8429 (ptp90) REVERT: D 164 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: D 283 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8163 (mt) REVERT: E 164 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: G 164 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: G 283 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8167 (mt) REVERT: H 164 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: I 58 ARG cc_start: 0.8678 (ptp90) cc_final: 0.8365 (ptp90) REVERT: J 164 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: J 283 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8164 (mt) REVERT: K 164 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7929 (m-80) outliers start: 93 outliers final: 37 residues processed: 436 average time/residue: 0.5081 time to fit residues: 335.1721 Evaluate side-chains 396 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 347 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 225 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 139 THR Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 225 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 164 TYR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 238 ILE 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 273 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 164 TYR Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 225 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 298 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 313 optimal weight: 0.6980 chunk 320 optimal weight: 7.9990 chunk 266 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 267 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN C 199 ASN D 309 ASN E 15 GLN F 199 ASN H 15 GLN I 199 ASN J 309 ASN K 15 GLN L 199 ASN L 218 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.219031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170718 restraints weight = 39937.232| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.90 r_work: 0.3900 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33264 Z= 0.119 Angle : 0.533 7.242 45288 Z= 0.269 Chirality : 0.043 0.164 5292 Planarity : 0.004 0.045 5868 Dihedral : 4.299 20.841 4512 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.70 % Allowed : 16.93 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 4272 helix: 1.67 (0.12), residues: 1920 sheet: -1.94 (0.21), residues: 552 loop : -1.56 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 147 HIS 0.002 0.000 HIS H 363 PHE 0.021 0.002 PHE B 367 TYR 0.006 0.001 TYR A 253 ARG 0.004 0.000 ARG G 58 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 1501) hydrogen bonds : angle 4.52931 ( 4251) covalent geometry : bond 0.00271 (33264) covalent geometry : angle 0.53262 (45288) *********************** 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 435 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 3.818 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: 0.7178 (m90) cc_final: 0.6852 (m90) REVERT: A 40 VAL cc_start: 0.7298 (p) cc_final: 0.7012 (p) REVERT: B 164 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: C 58 ARG cc_start: 0.8783 (ptp90) cc_final: 0.8463 (ptp90) REVERT: D 40 VAL cc_start: 0.7303 (p) cc_final: 0.7017 (p) REVERT: E 164 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: F 292 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6511 (pt0) REVERT: G 40 VAL cc_start: 0.7303 (p) cc_final: 0.7017 (p) REVERT: H 164 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: I 58 ARG cc_start: 0.8796 (ptp90) cc_final: 0.8479 (ptp90) REVERT: I 155 HIS cc_start: 0.7374 (m170) cc_final: 0.7124 (m170) REVERT: J 40 VAL cc_start: 0.7299 (p) cc_final: 0.7012 (p) REVERT: K 164 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7710 (m-80) outliers start: 57 outliers final: 20 residues processed: 415 average time/residue: 0.5326 time to fit residues: 330.1362 Evaluate side-chains 385 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 255 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 310 optimal weight: 0.5980 chunk 134 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 307 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.219167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.165541 restraints weight = 39984.361| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.02 r_work: 0.3889 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33264 Z= 0.129 Angle : 0.544 9.457 45288 Z= 0.275 Chirality : 0.043 0.150 5292 Planarity : 0.005 0.044 5868 Dihedral : 4.145 19.936 4512 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.49 % Allowed : 17.11 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 4272 helix: 1.82 (0.12), residues: 1932 sheet: -1.85 (0.21), residues: 552 loop : -1.51 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 147 HIS 0.002 0.001 HIS H 363 PHE 0.026 0.002 PHE H 367 TYR 0.008 0.001 TYR C 179 ARG 0.005 0.000 ARG G 58 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 1501) hydrogen bonds : angle 4.50933 ( 4251) covalent geometry : bond 0.00308 (33264) covalent geometry : angle 0.54433 (45288) *********************** 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 424 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 374 time to evaluate : 3.762 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: 0.7195 (m90) cc_final: 0.6863 (m90) REVERT: A 40 VAL cc_start: 0.7408 (p) cc_final: 0.7099 (p) REVERT: A 164 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: B 58 ARG cc_start: 0.8482 (ptp90) cc_final: 0.8088 (ptp90) REVERT: B 164 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: C 58 ARG cc_start: 0.8779 (ptp90) cc_final: 0.8429 (ptp90) REVERT: C 155 HIS cc_start: 0.7392 (m170) cc_final: 0.7149 (m170) REVERT: C 292 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6416 (pt0) REVERT: D 21 HIS cc_start: 0.7190 (m90) cc_final: 0.6856 (m90) REVERT: D 40 VAL cc_start: 0.7421 (p) cc_final: 0.7114 (p) REVERT: E 58 ARG cc_start: 0.8489 (ptp90) cc_final: 0.8093 (ptp90) REVERT: E 164 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: F 58 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8525 (ptp90) REVERT: G 40 VAL cc_start: 0.7419 (p) cc_final: 0.7109 (p) REVERT: G 164 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: H 58 ARG cc_start: 0.8475 (ptp90) cc_final: 0.8080 (ptp90) REVERT: H 164 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: H 200 LYS cc_start: 0.7781 (ptpp) cc_final: 0.7575 (pttp) REVERT: I 58 ARG cc_start: 0.8786 (ptp90) cc_final: 0.8437 (ptp90) REVERT: I 155 HIS cc_start: 0.7343 (m170) cc_final: 0.7116 (m170) REVERT: I 292 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: J 40 VAL cc_start: 0.7414 (p) cc_final: 0.7108 (p) REVERT: K 58 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8110 (ptp90) REVERT: K 164 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: K 200 LYS cc_start: 0.7786 (ptpp) cc_final: 0.7561 (pttp) REVERT: L 58 ARG cc_start: 0.8740 (ptp90) cc_final: 0.8501 (ptp90) REVERT: L 292 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6518 (pt0) outliers start: 50 outliers final: 24 residues processed: 403 average time/residue: 0.5304 time to fit residues: 320.0454 Evaluate side-chains 389 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 356 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 292 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 422 optimal weight: 0.9980 chunk 309 optimal weight: 0.1980 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 384 optimal weight: 0.9980 chunk 393 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 HIS E 14 GLN J 44 HIS K 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.222101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.175561 restraints weight = 39980.014| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.84 r_work: 0.3943 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33264 Z= 0.098 Angle : 0.513 10.367 45288 Z= 0.254 Chirality : 0.042 0.148 5292 Planarity : 0.004 0.044 5868 Dihedral : 3.803 21.174 4512 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.43 % Allowed : 17.71 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 4272 helix: 1.96 (0.12), residues: 1932 sheet: -1.71 (0.21), residues: 552 loop : -1.34 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 147 HIS 0.002 0.000 HIS J 142 PHE 0.027 0.001 PHE H 367 TYR 0.009 0.001 TYR J 253 ARG 0.005 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.02703 ( 1501) hydrogen bonds : angle 4.31799 ( 4251) covalent geometry : bond 0.00226 (33264) covalent geometry : angle 0.51255 (45288) *********************** 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 427 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 379 time to evaluate : 3.760 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: 0.7182 (m90) cc_final: 0.6868 (m90) REVERT: A 40 VAL cc_start: 0.7278 (p) cc_final: 0.6965 (p) REVERT: A 200 LYS cc_start: 0.7908 (ptpp) cc_final: 0.7620 (ptmm) REVERT: B 58 ARG cc_start: 0.8566 (ptp90) cc_final: 0.8183 (ptp90) REVERT: B 155 HIS cc_start: 0.7311 (m170) cc_final: 0.7068 (m170) REVERT: B 164 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: C 40 VAL cc_start: 0.7470 (p) cc_final: 0.7252 (p) REVERT: C 58 ARG cc_start: 0.8762 (ptp90) cc_final: 0.8408 (ptp90) REVERT: C 155 HIS cc_start: 0.7372 (m170) cc_final: 0.7104 (m170) REVERT: D 21 HIS cc_start: 0.7108 (m90) cc_final: 0.6783 (m90) REVERT: D 40 VAL cc_start: 0.7278 (p) cc_final: 0.6952 (p) REVERT: D 164 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: D 200 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7614 (ptmm) REVERT: E 14 GLN cc_start: 0.4612 (OUTLIER) cc_final: 0.3869 (mt0) REVERT: E 21 HIS cc_start: 0.7118 (m90) cc_final: 0.6714 (m90) REVERT: E 58 ARG cc_start: 0.8522 (ptp90) cc_final: 0.8150 (ptp90) REVERT: E 155 HIS cc_start: 0.7291 (m170) cc_final: 0.7057 (m170) REVERT: E 164 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: F 40 VAL cc_start: 0.7467 (p) cc_final: 0.7256 (p) REVERT: F 58 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8467 (ptp90) REVERT: G 21 HIS cc_start: 0.7111 (m90) cc_final: 0.6784 (m90) REVERT: G 40 VAL cc_start: 0.7285 (p) cc_final: 0.6973 (p) REVERT: G 200 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7615 (ptmm) REVERT: H 21 HIS cc_start: 0.7117 (m90) cc_final: 0.6737 (m90) REVERT: H 58 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8145 (ptp90) REVERT: H 155 HIS cc_start: 0.7283 (m170) cc_final: 0.7055 (m170) REVERT: H 164 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: I 40 VAL cc_start: 0.7458 (p) cc_final: 0.7234 (p) REVERT: I 58 ARG cc_start: 0.8776 (ptp90) cc_final: 0.8419 (ptp90) REVERT: I 155 HIS cc_start: 0.7353 (m170) cc_final: 0.7138 (m170) REVERT: J 21 HIS cc_start: 0.7102 (m90) cc_final: 0.6783 (m90) REVERT: J 40 VAL cc_start: 0.7275 (p) cc_final: 0.6963 (p) REVERT: J 164 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: J 200 LYS cc_start: 0.7903 (ptpp) cc_final: 0.7626 (ptmm) REVERT: K 14 GLN cc_start: 0.4600 (OUTLIER) cc_final: 0.3861 (mt0) REVERT: K 58 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8156 (ptp90) REVERT: K 155 HIS cc_start: 0.7309 (m170) cc_final: 0.7073 (m170) REVERT: K 164 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: L 40 VAL cc_start: 0.7468 (p) cc_final: 0.7255 (p) REVERT: L 58 ARG cc_start: 0.8732 (ptp90) cc_final: 0.8456 (ptp90) outliers start: 48 outliers final: 21 residues processed: 412 average time/residue: 0.5256 time to fit residues: 324.6617 Evaluate side-chains 391 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 362 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 164 TYR Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 255 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 90 optimal weight: 1.9990 chunk 364 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 chunk 228 optimal weight: 0.1980 chunk 274 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS B 14 GLN D 14 GLN E 14 GLN G 14 GLN G 44 HIS H 14 GLN J 14 GLN K 14 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.215249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.160215 restraints weight = 40089.032| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.97 r_work: 0.3863 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33264 Z= 0.216 Angle : 0.625 9.706 45288 Z= 0.316 Chirality : 0.046 0.164 5292 Planarity : 0.005 0.043 5868 Dihedral : 4.530 23.784 4512 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.47 % Allowed : 16.82 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 4272 helix: 1.77 (0.12), residues: 1932 sheet: -2.00 (0.22), residues: 552 loop : -1.49 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP K 147 HIS 0.002 0.001 HIS K 363 PHE 0.021 0.003 PHE H 367 TYR 0.014 0.002 TYR C 179 ARG 0.007 0.001 ARG L 204 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1501) hydrogen bonds : angle 4.67781 ( 4251) covalent geometry : bond 0.00518 (33264) covalent geometry : angle 0.62524 (45288) *********************** 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 466 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 383 time to evaluate : 3.375 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: 0.7139 (m90) cc_final: 0.6823 (m90) REVERT: A 40 VAL cc_start: 0.7428 (p) cc_final: 0.7093 (p) REVERT: A 58 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8194 (ptp90) REVERT: A 164 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: A 200 LYS cc_start: 0.7967 (ptpp) cc_final: 0.7654 (ptmm) REVERT: B 14 GLN cc_start: 0.4617 (OUTLIER) cc_final: 0.3942 (mt0) REVERT: B 21 HIS cc_start: 0.6979 (m90) cc_final: 0.6628 (m90) REVERT: B 58 ARG cc_start: 0.8600 (ptp90) cc_final: 0.8194 (ptp90) REVERT: B 155 HIS cc_start: 0.7325 (m170) cc_final: 0.7071 (m170) REVERT: B 164 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: C 56 LEU cc_start: 0.8047 (mt) cc_final: 0.7807 (mt) REVERT: C 58 ARG cc_start: 0.8768 (ptp90) cc_final: 0.8399 (ptp90) REVERT: C 155 HIS cc_start: 0.7316 (m170) cc_final: 0.7044 (m170) REVERT: C 200 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7597 (ptmm) REVERT: D 21 HIS cc_start: 0.7103 (m90) cc_final: 0.6789 (m90) REVERT: D 40 VAL cc_start: 0.7396 (p) cc_final: 0.7060 (p) REVERT: D 58 ARG cc_start: 0.8590 (ptp90) cc_final: 0.8327 (ptp90) REVERT: D 164 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: D 200 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7660 (ptmm) REVERT: E 21 HIS cc_start: 0.6994 (m90) cc_final: 0.6658 (m90) REVERT: E 58 ARG cc_start: 0.8611 (ptp90) cc_final: 0.8203 (ptp90) REVERT: E 155 HIS cc_start: 0.7329 (m170) cc_final: 0.7065 (m170) REVERT: E 164 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: F 21 HIS cc_start: 0.7144 (m90) cc_final: 0.6833 (m170) REVERT: F 58 ARG cc_start: 0.8717 (ptp90) cc_final: 0.8428 (ptp90) REVERT: F 200 LYS cc_start: 0.7881 (ptpp) cc_final: 0.7610 (ptmm) REVERT: G 21 HIS cc_start: 0.7104 (m90) cc_final: 0.6790 (m90) REVERT: G 40 VAL cc_start: 0.7434 (p) cc_final: 0.7099 (p) REVERT: G 58 ARG cc_start: 0.8501 (ptp90) cc_final: 0.8180 (ptp90) REVERT: G 164 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: G 200 LYS cc_start: 0.7956 (ptpp) cc_final: 0.7648 (ptmm) REVERT: H 14 GLN cc_start: 0.4648 (OUTLIER) cc_final: 0.3948 (mt0) REVERT: H 21 HIS cc_start: 0.6974 (m90) cc_final: 0.6633 (m90) REVERT: H 58 ARG cc_start: 0.8600 (ptp90) cc_final: 0.8195 (ptp90) REVERT: H 155 HIS cc_start: 0.7341 (m170) cc_final: 0.7076 (m170) REVERT: H 164 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: H 200 LYS cc_start: 0.7340 (ptmt) cc_final: 0.7106 (ptpp) REVERT: I 56 LEU cc_start: 0.8044 (mt) cc_final: 0.7805 (mt) REVERT: I 58 ARG cc_start: 0.8758 (ptp90) cc_final: 0.8399 (ptp90) REVERT: I 155 HIS cc_start: 0.7381 (m170) cc_final: 0.7161 (m170) REVERT: I 200 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7611 (ptmm) REVERT: J 21 HIS cc_start: 0.7107 (m90) cc_final: 0.6786 (m90) REVERT: J 40 VAL cc_start: 0.7420 (p) cc_final: 0.7085 (p) REVERT: J 58 ARG cc_start: 0.8507 (ptp90) cc_final: 0.8187 (ptp90) REVERT: J 164 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: J 200 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7654 (ptmm) REVERT: K 21 HIS cc_start: 0.7006 (m90) cc_final: 0.6659 (m90) REVERT: K 58 ARG cc_start: 0.8609 (ptp90) cc_final: 0.8201 (ptp90) REVERT: K 155 HIS cc_start: 0.7323 (m170) cc_final: 0.7069 (m170) REVERT: K 164 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: L 21 HIS cc_start: 0.7153 (m90) cc_final: 0.6832 (m170) REVERT: L 58 ARG cc_start: 0.8696 (ptp90) cc_final: 0.8414 (ptp90) REVERT: L 200 LYS cc_start: 0.7859 (ptpp) cc_final: 0.7596 (ptmm) outliers start: 83 outliers final: 45 residues processed: 450 average time/residue: 0.4940 time to fit residues: 336.5276 Evaluate side-chains 424 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 369 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 255 VAL 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 255 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 255 VAL 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 151 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 255 VAL 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 255 VAL Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 164 TYR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 255 VAL 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 255 VAL Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 25 optimal weight: 0.7980 chunk 341 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 346 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 314 optimal weight: 0.9980 chunk 362 optimal weight: 1.9990 chunk 420 optimal weight: 0.7980 chunk 33 optimal weight: 0.0020 chunk 60 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN H 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.220621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175644 restraints weight = 39908.871| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.61 r_work: 0.3951 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33264 Z= 0.101 Angle : 0.540 10.741 45288 Z= 0.266 Chirality : 0.043 0.167 5292 Planarity : 0.004 0.043 5868 Dihedral : 3.948 22.316 4512 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.46 % Allowed : 18.54 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 4272 helix: 1.94 (0.12), residues: 1932 sheet: -1.78 (0.22), residues: 552 loop : -1.37 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 147 HIS 0.002 0.000 HIS E 142 PHE 0.028 0.001 PHE B 367 TYR 0.009 0.001 TYR J 253 ARG 0.006 0.001 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 1501) hydrogen bonds : angle 4.42115 ( 4251) covalent geometry : bond 0.00234 (33264) covalent geometry : angle 0.53986 (45288) *********************** 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 448 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 3.615 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: 0.7131 (m90) cc_final: 0.6858 (m90) REVERT: A 40 VAL cc_start: 0.7313 (p) cc_final: 0.6992 (p) REVERT: A 58 ARG cc_start: 0.8431 (ptp90) cc_final: 0.8146 (ptp90) REVERT: B 21 HIS cc_start: 0.6998 (m90) cc_final: 0.6736 (m90) REVERT: B 155 HIS cc_start: 0.7255 (m170) cc_final: 0.7009 (m170) REVERT: B 164 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: C 40 VAL cc_start: 0.7497 (p) cc_final: 0.7294 (p) REVERT: C 58 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8405 (ptp90) REVERT: C 155 HIS cc_start: 0.7378 (m170) cc_final: 0.7114 (m170) REVERT: D 21 HIS cc_start: 0.7087 (m90) cc_final: 0.6789 (m90) REVERT: D 40 VAL cc_start: 0.7306 (OUTLIER) cc_final: 0.6983 (p) REVERT: D 58 ARG cc_start: 0.8630 (ptp90) cc_final: 0.8324 (ptp90) REVERT: E 21 HIS cc_start: 0.7033 (m90) cc_final: 0.6746 (m90) REVERT: E 155 HIS cc_start: 0.7231 (m170) cc_final: 0.6994 (m170) REVERT: E 164 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: F 21 HIS cc_start: 0.7142 (m90) cc_final: 0.6840 (m170) REVERT: F 40 VAL cc_start: 0.7595 (p) cc_final: 0.7387 (p) REVERT: F 58 ARG cc_start: 0.8704 (ptp90) cc_final: 0.8467 (ptp90) REVERT: G 21 HIS cc_start: 0.7080 (m90) cc_final: 0.6774 (m90) REVERT: G 40 VAL cc_start: 0.7301 (p) cc_final: 0.6980 (p) REVERT: G 58 ARG cc_start: 0.8424 (ptp90) cc_final: 0.8142 (ptp90) REVERT: H 21 HIS cc_start: 0.6992 (m90) cc_final: 0.6733 (m90) REVERT: H 155 HIS cc_start: 0.7235 (m170) cc_final: 0.6991 (m170) REVERT: H 164 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: H 200 LYS cc_start: 0.7505 (ptmt) cc_final: 0.7244 (ptpp) REVERT: I 40 VAL cc_start: 0.7509 (p) cc_final: 0.7301 (p) REVERT: I 58 ARG cc_start: 0.8747 (ptp90) cc_final: 0.8412 (ptp90) REVERT: I 155 HIS cc_start: 0.7311 (m170) cc_final: 0.7097 (m170) REVERT: J 21 HIS cc_start: 0.7079 (m90) cc_final: 0.6774 (m90) REVERT: J 40 VAL cc_start: 0.7301 (p) cc_final: 0.6979 (p) REVERT: J 58 ARG cc_start: 0.8426 (ptp90) cc_final: 0.8142 (ptp90) REVERT: K 21 HIS cc_start: 0.7021 (m90) cc_final: 0.6721 (m90) REVERT: K 155 HIS cc_start: 0.7243 (m170) cc_final: 0.7000 (m170) REVERT: K 164 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: L 21 HIS cc_start: 0.7141 (m90) cc_final: 0.6841 (m170) REVERT: L 40 VAL cc_start: 0.7492 (p) cc_final: 0.7286 (p) REVERT: L 58 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8422 (ptp90) outliers start: 49 outliers final: 28 residues processed: 432 average time/residue: 0.4957 time to fit residues: 324.0985 Evaluate side-chains 422 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 389 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 255 VAL 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 E residue 139 THR Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 255 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 228 optimal weight: 2.9990 chunk 389 optimal weight: 0.0870 chunk 349 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 310 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 306 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN E 14 GLN G 14 GLN J 14 GLN K 14 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.221137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.172275 restraints weight = 39920.378| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.98 r_work: 0.3930 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33264 Z= 0.103 Angle : 0.556 12.082 45288 Z= 0.269 Chirality : 0.043 0.198 5292 Planarity : 0.005 0.055 5868 Dihedral : 3.849 22.592 4512 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.43 % Allowed : 18.72 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 4272 helix: 1.97 (0.12), residues: 1932 sheet: -1.69 (0.22), residues: 552 loop : -1.32 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 147 HIS 0.002 0.001 HIS J 239 PHE 0.028 0.001 PHE B 367 TYR 0.008 0.001 TYR G 253 ARG 0.006 0.001 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.02764 ( 1501) hydrogen bonds : angle 4.36983 ( 4251) covalent geometry : bond 0.00241 (33264) covalent geometry : angle 0.55602 (45288) ********************** 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 441 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 393 time to evaluate : 3.605 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: 0.7139 (m90) cc_final: 0.6839 (m90) REVERT: A 40 VAL cc_start: 0.7211 (p) cc_final: 0.6880 (p) REVERT: A 58 ARG cc_start: 0.8427 (ptp90) cc_final: 0.8149 (ptp90) REVERT: B 21 HIS cc_start: 0.7010 (m90) cc_final: 0.6736 (m90) REVERT: B 164 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: C 40 VAL cc_start: 0.7504 (p) cc_final: 0.7294 (p) REVERT: C 58 ARG cc_start: 0.8765 (ptp90) cc_final: 0.8437 (ptp90) REVERT: C 155 HIS cc_start: 0.7396 (m170) cc_final: 0.7115 (m170) REVERT: D 21 HIS cc_start: 0.7081 (m90) cc_final: 0.6777 (m90) REVERT: D 40 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6888 (p) REVERT: E 21 HIS cc_start: 0.7011 (m90) cc_final: 0.6729 (m90) REVERT: E 164 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: F 21 HIS cc_start: 0.7119 (m90) cc_final: 0.6814 (m170) REVERT: F 40 VAL cc_start: 0.7538 (p) cc_final: 0.7305 (p) REVERT: F 43 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7415 (mmp-170) REVERT: G 21 HIS cc_start: 0.7094 (m90) cc_final: 0.6789 (m90) REVERT: G 40 VAL cc_start: 0.7198 (p) cc_final: 0.6867 (p) REVERT: G 58 ARG cc_start: 0.8441 (ptp90) cc_final: 0.8161 (ptp90) REVERT: H 21 HIS cc_start: 0.6967 (m90) cc_final: 0.6684 (m90) REVERT: H 164 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: H 200 LYS cc_start: 0.7661 (ptmt) cc_final: 0.7395 (ptpp) REVERT: I 21 HIS cc_start: 0.7127 (m90) cc_final: 0.6823 (m170) REVERT: I 40 VAL cc_start: 0.7574 (p) cc_final: 0.7347 (p) REVERT: I 43 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7512 (mmp80) REVERT: I 58 ARG cc_start: 0.8763 (ptp90) cc_final: 0.8446 (ptp90) REVERT: I 155 HIS cc_start: 0.7367 (m170) cc_final: 0.7153 (m170) REVERT: J 21 HIS cc_start: 0.7078 (m90) cc_final: 0.6772 (m90) REVERT: J 40 VAL cc_start: 0.7193 (p) cc_final: 0.6863 (p) REVERT: J 58 ARG cc_start: 0.8434 (ptp90) cc_final: 0.8157 (ptp90) REVERT: K 21 HIS cc_start: 0.6991 (m90) cc_final: 0.6712 (m90) REVERT: K 164 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: L 21 HIS cc_start: 0.7132 (m90) cc_final: 0.6819 (m170) REVERT: L 40 VAL cc_start: 0.7528 (p) cc_final: 0.7297 (p) REVERT: L 43 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.7409 (mmp-170) REVERT: L 58 ARG cc_start: 0.8709 (ptp90) cc_final: 0.8503 (ptp90) outliers start: 48 outliers final: 28 residues processed: 427 average time/residue: 0.5131 time to fit residues: 332.3932 Evaluate side-chains 408 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 255 VAL 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 E residue 139 THR Chi-restraints excluded: chain E residue 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 255 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 3 optimal weight: 5.9990 chunk 259 optimal weight: 0.0570 chunk 370 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 314 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 374 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 GLN K 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.218567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.169829 restraints weight = 40063.268| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.85 r_work: 0.3925 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33264 Z= 0.144 Angle : 0.596 11.928 45288 Z= 0.294 Chirality : 0.044 0.204 5292 Planarity : 0.005 0.065 5868 Dihedral : 4.112 22.185 4512 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.49 % Allowed : 18.93 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 4272 helix: 1.92 (0.12), residues: 1932 sheet: -1.76 (0.22), residues: 552 loop : -1.34 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 147 HIS 0.001 0.000 HIS H 142 PHE 0.026 0.002 PHE B 367 TYR 0.010 0.002 TYR C 179 ARG 0.008 0.001 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1501) hydrogen bonds : angle 4.53059 ( 4251) covalent geometry : bond 0.00346 (33264) covalent geometry : angle 0.59625 (45288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17685.10 seconds wall clock time: 306 minutes 30.81 seconds (18390.81 seconds total)