Starting phenix.real_space_refine on Sat Jun 28 01:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9l_37374/06_2025/8w9l_37374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9l_37374/06_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_37374/06_2025/8w9l_37374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9l_37374/06_2025/8w9l_37374.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9l_37374/06_2025/8w9l_37374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9l_37374/06_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-5710/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: 10.13, per 1000 atoms: 0.31 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: 8.80 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: 4.17 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: 12.06 Time building geometry restraints manager: 10.26 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: 0.28 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: 2.820 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: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 63.620 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.300 ------------------------------------------------------------------------------- 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 : 3.566 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: 0.5195 time to fit residues: 407.9486 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 : 3.752 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.170108 restraints weight = 40292.740| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.68 r_work: 0.3900 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 4.203 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: 0.8810 (mmm) cc_final: 0.8440 (tpp) REVERT: C 155 HIS cc_start: 0.7085 (m170) cc_final: 0.6864 (m170) REVERT: D 73 MET cc_start: 0.8813 (mmm) cc_final: 0.8443 (tpp) REVERT: G 73 MET cc_start: 0.8809 (mmm) cc_final: 0.8439 (tpp) REVERT: I 155 HIS cc_start: 0.7099 (m170) cc_final: 0.6893 (m170) REVERT: J 73 MET cc_start: 0.8812 (mmm) cc_final: 0.8442 (tpp) REVERT: L 155 HIS cc_start: 0.6927 (m170) cc_final: 0.6722 (m-70) outliers start: 61 outliers final: 18 residues processed: 431 average time/residue: 0.6088 time to fit residues: 405.6438 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 : 6.180 ------------------------------------------------------------------------------- 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: 0.8980 chunk 73 optimal weight: 5.9990 chunk 348 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 418 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 416 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 E 218 GLN F 218 GLN G 15 GLN G 218 GLN H 218 GLN I 218 GLN J 15 GLN J 218 GLN K 218 GLN L 218 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.221762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.169230 restraints weight = 39960.811| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.96 r_work: 0.3936 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33264 Z= 0.109 Angle : 0.502 6.456 45288 Z= 0.257 Chirality : 0.042 0.138 5292 Planarity : 0.004 0.048 5868 Dihedral : 4.023 17.567 4512 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.43 % Allowed : 10.33 % Favored : 88.24 % 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: 0.10 (0.14), residues: 4272 helix: 1.81 (0.12), residues: 1920 sheet: -1.60 (0.21), residues: 552 loop : -1.32 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 147 HIS 0.002 0.000 HIS B 142 PHE 0.023 0.002 PHE E 367 TYR 0.006 0.001 TYR A 179 ARG 0.004 0.000 ARG D 194 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 1501) hydrogen bonds : angle 4.37347 ( 4251) covalent geometry : bond 0.00248 (33264) covalent geometry : angle 0.50154 (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 446 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 398 time to evaluate : 4.042 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: 0.7452 (OUTLIER) cc_final: 0.7153 (p) REVERT: A 73 MET cc_start: 0.8854 (mmm) cc_final: 0.8473 (tpp) REVERT: A 155 HIS cc_start: 0.7048 (m170) cc_final: 0.6845 (m-70) REVERT: B 15 GLN cc_start: 0.5350 (mp10) cc_final: 0.4739 (mp10) REVERT: C 40 VAL cc_start: 0.7546 (p) cc_final: 0.7331 (p) REVERT: C 155 HIS cc_start: 0.7125 (m170) cc_final: 0.6921 (m170) REVERT: C 198 GLU cc_start: 0.5845 (pt0) cc_final: 0.5642 (pp20) REVERT: C 292 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6549 (pt0) REVERT: D 40 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7150 (p) REVERT: D 73 MET cc_start: 0.8856 (mmm) cc_final: 0.8479 (tpp) REVERT: D 155 HIS cc_start: 0.7032 (m170) cc_final: 0.6829 (m-70) REVERT: E 15 GLN cc_start: 0.5344 (mp10) cc_final: 0.4739 (mp10) REVERT: F 40 VAL cc_start: 0.7554 (p) cc_final: 0.7340 (p) REVERT: F 292 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6664 (pt0) REVERT: G 40 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.7144 (p) REVERT: G 73 MET cc_start: 0.8854 (mmm) cc_final: 0.8474 (tpp) REVERT: G 155 HIS cc_start: 0.7051 (m170) cc_final: 0.6846 (m-70) REVERT: H 15 GLN cc_start: 0.5340 (mp10) cc_final: 0.4724 (mp10) REVERT: I 40 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7337 (p) REVERT: I 198 GLU cc_start: 0.5871 (pt0) cc_final: 0.5662 (pp20) REVERT: I 292 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6659 (pt0) REVERT: J 40 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7143 (p) REVERT: J 73 MET cc_start: 0.8849 (mmm) cc_final: 0.8468 (tpp) REVERT: J 155 HIS cc_start: 0.7024 (m170) cc_final: 0.6820 (m-70) REVERT: K 15 GLN cc_start: 0.5342 (mp10) cc_final: 0.4732 (mp10) REVERT: L 40 VAL cc_start: 0.7532 (p) cc_final: 0.7318 (p) REVERT: L 198 GLU cc_start: 0.5856 (pt0) cc_final: 0.5650 (pp20) REVERT: L 292 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6561 (pt0) outliers start: 48 outliers final: 19 residues processed: 415 average time/residue: 0.5241 time to fit residues: 328.7843 Evaluate side-chains 394 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 366 time to evaluate : 3.669 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 262 LEU 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 151 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 262 LEU 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 151 ILE Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 40 VAL 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 151 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain K residue 262 LEU 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: 6.9990 chunk 371 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 225 optimal weight: 0.0470 chunk 343 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 402 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 overall best weight: 3.5284 ------------------------------------------------------------------------------- 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 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 296 ASN L 44 HIS L 296 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.215019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.167808 restraints weight = 40128.829| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.62 r_work: 0.3879 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 33264 Z= 0.270 Angle : 0.650 6.543 45288 Z= 0.335 Chirality : 0.047 0.167 5292 Planarity : 0.005 0.046 5868 Dihedral : 4.850 25.196 4512 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.53 % Allowed : 13.48 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.13), residues: 4272 helix: 1.56 (0.12), residues: 1848 sheet: -1.95 (0.21), residues: 552 loop : -1.50 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 147 HIS 0.005 0.001 HIS H 363 PHE 0.021 0.003 PHE H 367 TYR 0.017 0.003 TYR F 179 ARG 0.003 0.001 ARG D 204 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1501) hydrogen bonds : angle 4.74312 ( 4251) covalent geometry : bond 0.00640 (33264) covalent geometry : angle 0.65044 (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 462 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 377 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: B 164 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: C 292 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6524 (pt0) REVERT: D 164 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: E 164 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: E 200 LYS cc_start: 0.7968 (ptpp) cc_final: 0.7757 (ptpp) REVERT: G 164 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: H 164 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: I 155 HIS cc_start: 0.7245 (m170) cc_final: 0.7028 (m170) REVERT: J 164 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: K 164 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7909 (m-80) outliers start: 85 outliers final: 31 residues processed: 436 average time/residue: 0.6038 time to fit residues: 400.4983 Evaluate side-chains 384 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 5.216 ------------------------------------------------------------------------------- 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 273 THR 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 262 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 TYR 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 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 273 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 TYR Chi-restraints excluded: chain H residue 195 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 273 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 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: 2.9990 chunk 116 optimal weight: 0.9980 chunk 313 optimal weight: 6.9990 chunk 320 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 110 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.218744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165724 restraints weight = 39935.860| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.30 r_work: 0.3893 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33264 Z= 0.128 Angle : 0.541 7.911 45288 Z= 0.272 Chirality : 0.043 0.161 5292 Planarity : 0.004 0.043 5868 Dihedral : 4.269 20.864 4512 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.55 % Allowed : 16.96 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.12), residues: 1920 sheet: -1.85 (0.21), residues: 552 loop : -1.45 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 147 HIS 0.002 0.000 HIS C 155 PHE 0.024 0.002 PHE H 367 TYR 0.008 0.001 TYR J 179 ARG 0.003 0.000 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 1501) hydrogen bonds : angle 4.48910 ( 4251) covalent geometry : bond 0.00299 (33264) covalent geometry : angle 0.54115 (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 413 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 4.176 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: 0.7211 (m90) cc_final: 0.6829 (m-70) REVERT: A 40 VAL cc_start: 0.7259 (p) cc_final: 0.6960 (p) REVERT: A 58 ARG cc_start: 0.8483 (ptp90) cc_final: 0.8234 (ptp90) REVERT: B 155 HIS cc_start: 0.7245 (m170) cc_final: 0.7027 (m170) REVERT: B 164 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: C 155 HIS cc_start: 0.7313 (m170) cc_final: 0.7020 (m170) REVERT: C 292 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6567 (pt0) REVERT: D 40 VAL cc_start: 0.7246 (p) cc_final: 0.6948 (p) REVERT: D 58 ARG cc_start: 0.8500 (ptp90) cc_final: 0.8253 (ptp90) REVERT: E 155 HIS cc_start: 0.7290 (m170) cc_final: 0.7082 (m170) REVERT: E 164 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: F 292 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6531 (pt0) REVERT: G 40 VAL cc_start: 0.7263 (p) cc_final: 0.6963 (p) REVERT: G 58 ARG cc_start: 0.8495 (ptp90) cc_final: 0.8244 (ptp90) REVERT: H 155 HIS cc_start: 0.7303 (m170) cc_final: 0.7095 (m170) REVERT: H 164 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: I 155 HIS cc_start: 0.7319 (m170) cc_final: 0.7100 (m170) REVERT: I 292 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: J 40 VAL cc_start: 0.7252 (p) cc_final: 0.6954 (p) REVERT: J 58 ARG cc_start: 0.8493 (ptp90) cc_final: 0.8242 (ptp90) REVERT: K 155 HIS cc_start: 0.7275 (m170) cc_final: 0.7063 (m170) REVERT: K 164 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: L 292 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6535 (pt0) outliers start: 52 outliers final: 20 residues processed: 393 average time/residue: 0.5585 time to fit residues: 327.0926 Evaluate side-chains 370 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 342 time to evaluate : 3.926 ------------------------------------------------------------------------------- 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 273 THR 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 164 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 292 GLN 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 273 THR 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 164 TYR Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 273 THR Chi-restraints excluded: chain L residue 292 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 310 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 334 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 341 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.219727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.164565 restraints weight = 39530.414| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.35 r_work: 0.3907 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33264 Z= 0.117 Angle : 0.526 8.648 45288 Z= 0.263 Chirality : 0.043 0.147 5292 Planarity : 0.004 0.043 5868 Dihedral : 4.029 20.167 4512 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.32 % Allowed : 16.79 % Favored : 80.89 % 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: 0.12 (0.14), residues: 4272 helix: 1.89 (0.12), residues: 1932 sheet: -1.77 (0.21), residues: 552 loop : -1.35 (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 H 363 PHE 0.025 0.002 PHE H 367 TYR 0.008 0.001 TYR G 253 ARG 0.004 0.000 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 1501) hydrogen bonds : angle 4.35283 ( 4251) covalent geometry : bond 0.00273 (33264) covalent geometry : angle 0.52606 (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 450 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 372 time to evaluate : 5.236 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: 0.7184 (m90) cc_final: 0.6856 (m90) REVERT: A 40 VAL cc_start: 0.7376 (p) cc_final: 0.7070 (p) REVERT: A 58 ARG cc_start: 0.8563 (ptp90) cc_final: 0.8274 (ptp90) REVERT: B 164 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: B 200 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7646 (pttp) REVERT: C 40 VAL cc_start: 0.7435 (p) cc_final: 0.7204 (p) REVERT: C 198 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6429 (pt0) REVERT: C 292 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6591 (pt0) REVERT: D 40 VAL cc_start: 0.7372 (p) cc_final: 0.7065 (p) REVERT: D 58 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8285 (ptp90) REVERT: E 164 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: F 40 VAL cc_start: 0.7444 (p) cc_final: 0.7215 (p) REVERT: G 40 VAL cc_start: 0.7379 (p) cc_final: 0.7072 (p) REVERT: G 58 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8280 (ptp90) REVERT: H 164 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: H 200 LYS cc_start: 0.7920 (ptpp) cc_final: 0.7634 (pttp) REVERT: I 155 HIS cc_start: 0.7325 (m170) cc_final: 0.7100 (m170) REVERT: J 40 VAL cc_start: 0.7367 (p) cc_final: 0.7061 (p) REVERT: J 58 ARG cc_start: 0.8569 (ptp90) cc_final: 0.8281 (ptp90) REVERT: K 164 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: L 40 VAL cc_start: 0.7428 (p) cc_final: 0.7199 (p) REVERT: L 198 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6483 (pt0) REVERT: L 292 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6576 (pt0) outliers start: 78 outliers final: 31 residues processed: 426 average time/residue: 0.7083 time to fit residues: 459.5302 Evaluate side-chains 388 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 351 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 139 THR 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 139 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 139 THR 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 139 THR 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 273 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 H residue 273 THR Chi-restraints excluded: chain I residue 139 THR 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 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 139 THR Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 273 THR 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: 4.9990 chunk 309 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 347 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 384 optimal weight: 4.9990 chunk 393 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN D 44 HIS I 199 ASN J 44 HIS L 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.221965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176519 restraints weight = 40020.197| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.74 r_work: 0.3952 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33264 Z= 0.103 Angle : 0.524 10.730 45288 Z= 0.260 Chirality : 0.042 0.146 5292 Planarity : 0.004 0.043 5868 Dihedral : 3.802 19.119 4512 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.67 % Allowed : 16.70 % Favored : 81.64 % 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: 0.26 (0.14), residues: 4272 helix: 1.99 (0.12), residues: 1932 sheet: -1.65 (0.21), residues: 552 loop : -1.28 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 147 HIS 0.002 0.000 HIS E 155 PHE 0.025 0.001 PHE H 367 TYR 0.009 0.001 TYR J 253 ARG 0.005 0.000 ARG F 194 Details of bonding type rmsd hydrogen bonds : bond 0.02796 ( 1501) hydrogen bonds : angle 4.31175 ( 4251) covalent geometry : bond 0.00241 (33264) covalent geometry : angle 0.52444 (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 445 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 389 time to evaluate : 4.134 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: 0.7135 (m90) cc_final: 0.6825 (m90) REVERT: A 40 VAL cc_start: 0.7264 (OUTLIER) cc_final: 0.6948 (p) REVERT: A 58 ARG cc_start: 0.8595 (ptp90) cc_final: 0.8380 (ptp90) REVERT: B 58 ARG cc_start: 0.8462 (ptp90) cc_final: 0.8111 (ptp90) REVERT: B 155 HIS cc_start: 0.7158 (m170) cc_final: 0.6885 (m170) REVERT: B 164 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 200 LYS cc_start: 0.7772 (ptpp) cc_final: 0.7570 (ptmm) REVERT: C 40 VAL cc_start: 0.7497 (p) cc_final: 0.7280 (p) REVERT: C 155 HIS cc_start: 0.7294 (m170) cc_final: 0.7072 (m170) REVERT: C 198 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6480 (pt0) REVERT: C 292 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6614 (pt0) REVERT: D 21 HIS cc_start: 0.7089 (m90) cc_final: 0.6779 (m90) REVERT: D 40 VAL cc_start: 0.7260 (OUTLIER) cc_final: 0.6943 (p) REVERT: D 58 ARG cc_start: 0.8586 (ptp90) cc_final: 0.8372 (ptp90) REVERT: E 58 ARG cc_start: 0.8474 (ptp90) cc_final: 0.8124 (ptp90) REVERT: E 155 HIS cc_start: 0.7161 (m170) cc_final: 0.6893 (m170) REVERT: E 164 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: F 40 VAL cc_start: 0.7490 (p) cc_final: 0.7273 (p) REVERT: F 197 GLU cc_start: 0.7454 (pm20) cc_final: 0.7165 (pm20) REVERT: G 21 HIS cc_start: 0.7095 (m90) cc_final: 0.6782 (m90) REVERT: G 40 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6959 (p) REVERT: G 58 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8373 (ptp90) REVERT: H 58 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8141 (ptp90) REVERT: H 155 HIS cc_start: 0.7154 (m170) cc_final: 0.6883 (m170) REVERT: H 164 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: I 40 VAL cc_start: 0.7584 (p) cc_final: 0.7340 (p) REVERT: I 155 HIS cc_start: 0.7238 (m170) cc_final: 0.7009 (m170) REVERT: I 194 ARG cc_start: 0.6254 (mtp180) cc_final: 0.6017 (ttm170) REVERT: J 21 HIS cc_start: 0.7096 (m90) cc_final: 0.6786 (m90) REVERT: J 40 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6922 (p) REVERT: J 58 ARG cc_start: 0.8587 (ptp90) cc_final: 0.8373 (ptp90) REVERT: K 58 ARG cc_start: 0.8483 (ptp90) cc_final: 0.8128 (ptp90) REVERT: K 155 HIS cc_start: 0.7193 (m170) cc_final: 0.6921 (m170) REVERT: K 164 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: K 200 LYS cc_start: 0.7768 (ptpp) cc_final: 0.7568 (ptmm) REVERT: L 40 VAL cc_start: 0.7483 (p) cc_final: 0.7267 (p) REVERT: L 198 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6479 (pt0) REVERT: L 292 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6617 (pt0) outliers start: 56 outliers final: 26 residues processed: 430 average time/residue: 0.5658 time to fit residues: 369.1246 Evaluate side-chains 401 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 365 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 B residue 273 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 139 THR 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 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 40 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 273 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 H residue 273 THR Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain J residue 40 VAL 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 K residue 273 THR Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 273 THR Chi-restraints excluded: chain L residue 292 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 90 optimal weight: 2.9990 chunk 364 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 E 14 GLN E 44 HIS G 44 HIS H 14 GLN K 14 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.217400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166496 restraints weight = 39967.318| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.93 r_work: 0.3886 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33264 Z= 0.175 Angle : 0.588 10.317 45288 Z= 0.294 Chirality : 0.045 0.154 5292 Planarity : 0.005 0.042 5868 Dihedral : 4.274 22.300 4512 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.08 % Allowed : 16.28 % Favored : 81.64 % 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: 0.05 (0.14), residues: 4272 helix: 1.83 (0.12), residues: 1932 sheet: -1.82 (0.22), residues: 552 loop : -1.38 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 147 HIS 0.002 0.001 HIS E 363 PHE 0.018 0.002 PHE H 367 TYR 0.011 0.002 TYR J 179 ARG 0.006 0.001 ARG L 204 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1501) hydrogen bonds : angle 4.51430 ( 4251) covalent geometry : bond 0.00418 (33264) covalent geometry : angle 0.58808 (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 442 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 3.987 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: A 21 HIS cc_start: 0.7181 (m90) cc_final: 0.6864 (m90) REVERT: A 40 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7059 (p) REVERT: A 58 ARG cc_start: 0.8640 (ptp90) cc_final: 0.8387 (ptp90) REVERT: A 164 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: B 14 GLN cc_start: 0.4673 (OUTLIER) cc_final: 0.3948 (mt0) REVERT: B 21 HIS cc_start: 0.6997 (m90) cc_final: 0.6655 (m90) REVERT: B 58 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8071 (ptp90) REVERT: B 164 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: C 40 VAL cc_start: 0.7512 (p) cc_final: 0.7286 (p) REVERT: C 58 ARG cc_start: 0.8786 (ptp90) cc_final: 0.8542 (ptp90) REVERT: C 155 HIS cc_start: 0.7320 (m170) cc_final: 0.7104 (m170) REVERT: C 200 LYS cc_start: 0.7895 (ptpp) cc_final: 0.7659 (ptmm) REVERT: D 21 HIS cc_start: 0.7125 (m90) cc_final: 0.6807 (m90) REVERT: D 40 VAL cc_start: 0.7398 (OUTLIER) cc_final: 0.7054 (p) REVERT: D 58 ARG cc_start: 0.8662 (ptp90) cc_final: 0.8407 (ptp90) REVERT: D 164 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: E 14 GLN cc_start: 0.4627 (OUTLIER) cc_final: 0.3898 (mt0) REVERT: E 21 HIS cc_start: 0.7043 (m90) cc_final: 0.6687 (m90) REVERT: E 58 ARG cc_start: 0.8492 (ptp90) cc_final: 0.8041 (ptp90) REVERT: E 164 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: F 21 HIS cc_start: 0.7173 (m90) cc_final: 0.6861 (m170) REVERT: F 40 VAL cc_start: 0.7492 (p) cc_final: 0.7262 (p) REVERT: F 58 ARG cc_start: 0.8780 (ptp90) cc_final: 0.8515 (ptp90) REVERT: F 80 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7443 (mmtt) REVERT: G 21 HIS cc_start: 0.7132 (m90) cc_final: 0.6813 (m90) REVERT: G 40 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7051 (p) REVERT: G 58 ARG cc_start: 0.8655 (ptp90) cc_final: 0.8400 (ptp90) REVERT: G 164 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: H 14 GLN cc_start: 0.4620 (OUTLIER) cc_final: 0.3891 (mt0) REVERT: H 21 HIS cc_start: 0.6987 (m90) cc_final: 0.6657 (m90) REVERT: H 58 ARG cc_start: 0.8484 (ptp90) cc_final: 0.8046 (ptp90) REVERT: H 164 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: I 58 ARG cc_start: 0.8793 (ptp90) cc_final: 0.8543 (ptp90) REVERT: I 155 HIS cc_start: 0.7322 (m170) cc_final: 0.7115 (m170) REVERT: J 21 HIS cc_start: 0.7130 (m90) cc_final: 0.6812 (m90) REVERT: J 40 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.7042 (p) REVERT: J 58 ARG cc_start: 0.8652 (ptp90) cc_final: 0.8399 (ptp90) REVERT: J 164 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: K 14 GLN cc_start: 0.4688 (OUTLIER) cc_final: 0.3957 (mt0) REVERT: K 21 HIS cc_start: 0.7011 (m90) cc_final: 0.6649 (m90) REVERT: K 58 ARG cc_start: 0.8520 (ptp90) cc_final: 0.8087 (ptp90) REVERT: K 164 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: L 40 VAL cc_start: 0.7500 (p) cc_final: 0.7272 (p) REVERT: L 58 ARG cc_start: 0.8765 (ptp90) cc_final: 0.8510 (ptp90) REVERT: L 200 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7635 (ptmm) outliers start: 70 outliers final: 33 residues processed: 422 average time/residue: 0.5128 time to fit residues: 331.0850 Evaluate side-chains 402 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 14 GLN 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 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 40 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 14 GLN 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 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 40 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain H residue 14 GLN 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 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 40 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 164 TYR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 14 GLN 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 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: 0.9990 chunk 341 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 346 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 362 optimal weight: 0.9990 chunk 420 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN G 14 GLN J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.221472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.174174 restraints weight = 39907.837| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.70 r_work: 0.3944 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33264 Z= 0.103 Angle : 0.546 11.562 45288 Z= 0.267 Chirality : 0.043 0.165 5292 Planarity : 0.004 0.043 5868 Dihedral : 3.864 21.612 4512 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.73 % Allowed : 17.08 % Favored : 81.19 % 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: 0.23 (0.14), residues: 4272 helix: 1.96 (0.12), residues: 1932 sheet: -1.66 (0.22), residues: 552 loop : -1.29 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 147 HIS 0.002 0.000 HIS K 142 PHE 0.029 0.001 PHE E 367 TYR 0.009 0.001 TYR A 253 ARG 0.006 0.000 ARG F 194 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 1501) hydrogen bonds : angle 4.36693 ( 4251) covalent geometry : bond 0.00239 (33264) covalent geometry : angle 0.54650 (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 444 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 386 time to evaluate : 4.189 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: 0.7136 (m90) cc_final: 0.6859 (m90) REVERT: A 40 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6882 (p) REVERT: B 21 HIS cc_start: 0.7007 (m90) cc_final: 0.6743 (m90) REVERT: B 58 ARG cc_start: 0.8503 (ptp90) cc_final: 0.8113 (ptp90) REVERT: B 155 HIS cc_start: 0.7290 (m170) cc_final: 0.7060 (m170) REVERT: B 164 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: C 40 VAL cc_start: 0.7621 (p) cc_final: 0.7308 (p) REVERT: C 58 ARG cc_start: 0.8764 (ptp90) cc_final: 0.8504 (ptp90) REVERT: C 155 HIS cc_start: 0.7289 (m170) cc_final: 0.7064 (m170) REVERT: C 194 ARG cc_start: 0.6225 (ttm170) cc_final: 0.5887 (ttt180) REVERT: D 21 HIS cc_start: 0.7077 (m90) cc_final: 0.6772 (m90) REVERT: D 40 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6877 (p) REVERT: E 21 HIS cc_start: 0.7013 (m90) cc_final: 0.6746 (m90) REVERT: E 58 ARG cc_start: 0.8485 (ptp90) cc_final: 0.8052 (ptp90) REVERT: E 155 HIS cc_start: 0.7279 (m170) cc_final: 0.7052 (m170) REVERT: E 164 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: F 21 HIS cc_start: 0.7132 (m90) cc_final: 0.6836 (m170) REVERT: F 40 VAL cc_start: 0.7611 (p) cc_final: 0.7398 (p) REVERT: F 58 ARG cc_start: 0.8752 (ptp90) cc_final: 0.8473 (ptp90) REVERT: F 194 ARG cc_start: 0.6476 (mtp180) cc_final: 0.6192 (ttm170) REVERT: F 200 LYS cc_start: 0.7918 (ptpp) cc_final: 0.7699 (ptmm) REVERT: G 21 HIS cc_start: 0.7087 (m90) cc_final: 0.6777 (m90) REVERT: G 40 VAL cc_start: 0.7218 (OUTLIER) cc_final: 0.6882 (p) REVERT: H 21 HIS cc_start: 0.6991 (m90) cc_final: 0.6741 (m90) REVERT: H 58 ARG cc_start: 0.8487 (ptp90) cc_final: 0.8054 (ptp90) REVERT: H 155 HIS cc_start: 0.7239 (m170) cc_final: 0.7008 (m170) REVERT: H 164 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: I 40 VAL cc_start: 0.7613 (p) cc_final: 0.7393 (p) REVERT: I 58 ARG cc_start: 0.8771 (ptp90) cc_final: 0.8510 (ptp90) REVERT: I 155 HIS cc_start: 0.7244 (m170) cc_final: 0.7031 (m170) REVERT: I 194 ARG cc_start: 0.6156 (ttm170) cc_final: 0.5939 (mtp180) REVERT: J 21 HIS cc_start: 0.7072 (m90) cc_final: 0.6770 (m90) REVERT: J 40 VAL cc_start: 0.7214 (OUTLIER) cc_final: 0.6880 (p) REVERT: K 21 HIS cc_start: 0.7005 (m90) cc_final: 0.6740 (m90) REVERT: K 58 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8125 (ptp90) REVERT: K 155 HIS cc_start: 0.7266 (m170) cc_final: 0.7036 (m170) REVERT: K 164 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: K 200 LYS cc_start: 0.7460 (ptmt) cc_final: 0.7167 (pttp) REVERT: L 21 HIS cc_start: 0.7147 (m90) cc_final: 0.6848 (m170) REVERT: L 40 VAL cc_start: 0.7601 (p) cc_final: 0.7388 (p) REVERT: L 58 ARG cc_start: 0.8754 (ptp90) cc_final: 0.8488 (ptp90) REVERT: L 194 ARG cc_start: 0.6201 (ttm170) cc_final: 0.5967 (mtp180) outliers start: 58 outliers final: 29 residues processed: 425 average time/residue: 0.5543 time to fit residues: 362.6798 Evaluate side-chains 401 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 364 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain 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 139 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain 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 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 40 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 273 THR 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 139 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 139 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 139 THR Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 228 optimal weight: 6.9990 chunk 389 optimal weight: 0.0670 chunk 349 optimal weight: 0.0970 chunk 196 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 310 optimal weight: 0.5980 chunk 326 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN D 14 GLN E 14 GLN G 14 GLN H 14 GLN J 14 GLN K 14 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.222783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.177808 restraints weight = 39780.375| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.72 r_work: 0.3986 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 33264 Z= 0.100 Angle : 0.569 12.347 45288 Z= 0.276 Chirality : 0.043 0.247 5292 Planarity : 0.005 0.064 5868 Dihedral : 3.754 29.988 4512 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.37 % Allowed : 17.86 % Favored : 80.77 % 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: 0.28 (0.14), residues: 4272 helix: 1.97 (0.12), residues: 1932 sheet: -1.55 (0.22), residues: 552 loop : -1.26 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 147 HIS 0.002 0.000 HIS K 142 PHE 0.028 0.001 PHE H 367 TYR 0.009 0.001 TYR A 253 ARG 0.009 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 1501) hydrogen bonds : angle 4.35360 ( 4251) covalent geometry : bond 0.00232 (33264) covalent geometry : angle 0.56935 (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 419 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 373 time to evaluate : 3.670 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: A 21 HIS cc_start: 0.7096 (m90) cc_final: 0.6815 (m90) REVERT: A 40 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6863 (p) REVERT: B 14 GLN cc_start: 0.4858 (OUTLIER) cc_final: 0.4122 (mt0) REVERT: B 21 HIS cc_start: 0.6884 (m90) cc_final: 0.6651 (m90) REVERT: B 58 ARG cc_start: 0.8476 (ptp90) cc_final: 0.8097 (ptp90) REVERT: B 164 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: C 58 ARG cc_start: 0.8687 (ptp90) cc_final: 0.8457 (ptp90) REVERT: C 155 HIS cc_start: 0.7285 (m170) cc_final: 0.7072 (m170) REVERT: D 21 HIS cc_start: 0.7022 (m90) cc_final: 0.6749 (m90) REVERT: D 40 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6867 (p) REVERT: E 14 GLN cc_start: 0.4618 (OUTLIER) cc_final: 0.3849 (mt0) REVERT: E 21 HIS cc_start: 0.6971 (m90) cc_final: 0.6705 (m90) REVERT: E 58 ARG cc_start: 0.8501 (ptp90) cc_final: 0.8115 (ptp90) REVERT: E 164 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: F 21 HIS cc_start: 0.7111 (m90) cc_final: 0.6841 (m170) REVERT: F 40 VAL cc_start: 0.7627 (p) cc_final: 0.7423 (p) REVERT: F 58 ARG cc_start: 0.8647 (ptp90) cc_final: 0.8426 (ptp90) REVERT: G 21 HIS cc_start: 0.7039 (m90) cc_final: 0.6761 (m90) REVERT: G 40 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6874 (p) REVERT: H 14 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.3869 (mt0) REVERT: H 21 HIS cc_start: 0.6894 (m90) cc_final: 0.6653 (m90) REVERT: H 58 ARG cc_start: 0.8480 (ptp90) cc_final: 0.8097 (ptp90) REVERT: H 164 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: I 40 VAL cc_start: 0.7578 (p) cc_final: 0.7363 (p) REVERT: I 43 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7480 (mmp80) REVERT: I 58 ARG cc_start: 0.8701 (ptp90) cc_final: 0.8454 (ptp90) REVERT: I 155 HIS cc_start: 0.7268 (m170) cc_final: 0.7056 (m170) REVERT: J 21 HIS cc_start: 0.7041 (m90) cc_final: 0.6759 (m90) REVERT: J 40 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6866 (p) REVERT: K 14 GLN cc_start: 0.4856 (OUTLIER) cc_final: 0.4125 (mt0) REVERT: K 21 HIS cc_start: 0.6870 (m90) cc_final: 0.6632 (m90) REVERT: K 58 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8119 (ptp90) REVERT: K 164 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: L 21 HIS cc_start: 0.7094 (m90) cc_final: 0.6821 (m170) REVERT: L 40 VAL cc_start: 0.7596 (p) cc_final: 0.7392 (p) REVERT: L 58 ARG cc_start: 0.8637 (ptp90) cc_final: 0.8425 (ptp90) outliers start: 46 outliers final: 29 residues processed: 409 average time/residue: 0.5253 time to fit residues: 326.9093 Evaluate side-chains 401 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 14 GLN 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 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 14 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 139 THR 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 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 14 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 14 GLN 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 139 THR Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain K residue 14 GLN 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 K residue 273 THR Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 3 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 370 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 373 optimal weight: 0.8980 chunk 342 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 374 optimal weight: 0.0870 chunk 199 optimal weight: 0.9980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN G 14 GLN J 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.222900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.174133 restraints weight = 40031.333| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.84 r_work: 0.3968 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 33264 Z= 0.229 Angle : 1.037 59.200 45288 Z= 0.616 Chirality : 0.045 0.585 5292 Planarity : 0.006 0.142 5868 Dihedral : 3.896 30.032 4512 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % Rotamer: Outliers : 1.37 % Allowed : 17.86 % Favored : 80.77 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.22 (0.14), residues: 4272 helix: 1.90 (0.12), residues: 1932 sheet: -1.55 (0.22), residues: 552 loop : -1.26 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 147 HIS 0.002 0.000 HIS C 142 PHE 0.027 0.002 PHE H 367 TYR 0.010 0.001 TYR G 253 ARG 0.009 0.001 ARG F 194 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 1501) hydrogen bonds : angle 4.36711 ( 4251) covalent geometry : bond 0.00475 (33264) covalent geometry : angle 1.03738 (45288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19052.04 seconds wall clock time: 335 minutes 20.99 seconds (20120.99 seconds total)