Starting phenix.real_space_refine on Wed Oct 28 15:29:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9szd_55366/10_2026/9szd_55366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9szd_55366/10_2026/9szd_55366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9szd_55366/10_2026/9szd_55366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9szd_55366/10_2026/9szd_55366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9szd_55366/10_2026/9szd_55366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9szd_55366/10_2026/9szd_55366.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 126 5.16 5 C 18252 2.51 5 N 4554 2.21 5 O 5724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28656 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Time building chain proxies: 3.33, per 1000 atoms: 0.12 Number of scatterers: 28656 At special positions: 0 Unit cell: (122.931, 119.799, 153.468, 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 126 16.00 O 5724 8.00 N 4554 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6732 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 72 sheets defined 12.9% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA E 212 " --> pdb=" O PRO E 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 85 Processing helix chain 'F' and resid 190 through 200 Processing helix chain 'F' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA F 212 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY F 213 " --> pdb=" O SER F 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 85 Processing helix chain 'G' and resid 190 through 200 Processing helix chain 'G' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA G 212 " --> pdb=" O PRO G 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 85 Processing helix chain 'H' and resid 190 through 200 Processing helix chain 'H' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA H 212 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY H 213 " --> pdb=" O SER H 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 85 Processing helix chain 'I' and resid 190 through 200 Processing helix chain 'I' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA I 212 " --> pdb=" O PRO I 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'J' and resid 190 through 200 Processing helix chain 'J' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA J 212 " --> pdb=" O PRO J 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY J 213 " --> pdb=" O SER J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 85 Processing helix chain 'K' and resid 190 through 200 Processing helix chain 'K' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA K 212 " --> pdb=" O PRO K 208 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY K 213 " --> pdb=" O SER K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 Processing helix chain 'L' and resid 190 through 200 Processing helix chain 'L' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA L 212 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY L 213 " --> pdb=" O SER L 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 85 Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'M' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA M 212 " --> pdb=" O PRO M 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY M 213 " --> pdb=" O SER M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 85 Processing helix chain 'N' and resid 190 through 200 Processing helix chain 'N' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA N 212 " --> pdb=" O PRO N 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY N 213 " --> pdb=" O SER N 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 85 Processing helix chain 'O' and resid 190 through 200 Processing helix chain 'O' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA O 212 " --> pdb=" O PRO O 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY O 213 " --> pdb=" O SER O 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 190 through 200 Processing helix chain 'P' and resid 207 through 214 removed outlier: 4.267A pdb=" N ALA P 212 " --> pdb=" O PRO P 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY P 213 " --> pdb=" O SER P 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 85 Processing helix chain 'Q' and resid 190 through 200 Processing helix chain 'Q' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA Q 212 " --> pdb=" O PRO Q 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY Q 213 " --> pdb=" O SER Q 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 85 Processing helix chain 'R' and resid 190 through 200 Processing helix chain 'R' and resid 207 through 214 removed outlier: 4.266A pdb=" N ALA R 212 " --> pdb=" O PRO R 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY R 213 " --> pdb=" O SER R 209 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 26 through 27 current: chain 'A' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 73 current: chain 'A' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 124 through 136 current: chain 'A' and resid 157 through 164 Processing sheet with id=2, first strand: chain 'A' and resid 47 through 50 Processing sheet with id=3, first strand: chain 'A' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA A 98 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA A 169 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 26 through 27 current: chain 'B' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 73 current: chain 'B' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 124 through 136 current: chain 'B' and resid 157 through 164 Processing sheet with id=6, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=7, first strand: chain 'B' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA B 98 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA B 169 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 26 through 27 current: chain 'C' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 66 through 73 current: chain 'C' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 124 through 136 current: chain 'C' and resid 157 through 164 Processing sheet with id=10, first strand: chain 'C' and resid 47 through 50 Processing sheet with id=11, first strand: chain 'C' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA C 98 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA C 169 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 26 through 27 current: chain 'D' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 73 current: chain 'D' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 124 through 136 current: chain 'D' and resid 157 through 164 Processing sheet with id=14, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=15, first strand: chain 'D' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA D 98 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA D 169 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 26 through 27 current: chain 'E' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 66 through 73 current: chain 'E' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 124 through 136 current: chain 'E' and resid 157 through 164 Processing sheet with id=18, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=19, first strand: chain 'E' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA E 98 " --> pdb=" O ILE E 91 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA E 169 " --> pdb=" O ARG E 176 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'F' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 26 through 27 current: chain 'F' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 73 current: chain 'F' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 124 through 136 current: chain 'F' and resid 157 through 164 Processing sheet with id=22, first strand: chain 'F' and resid 47 through 50 Processing sheet with id=23, first strand: chain 'F' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA F 98 " --> pdb=" O ILE F 91 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'F' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA F 169 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'G' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 26 through 27 current: chain 'G' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 66 through 73 current: chain 'G' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 124 through 136 current: chain 'G' and resid 157 through 164 Processing sheet with id=26, first strand: chain 'G' and resid 47 through 50 Processing sheet with id=27, first strand: chain 'G' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA G 98 " --> pdb=" O ILE G 91 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA G 169 " --> pdb=" O ARG G 176 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'H' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 26 through 27 current: chain 'H' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 66 through 73 current: chain 'H' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 124 through 136 current: chain 'H' and resid 157 through 164 Processing sheet with id=30, first strand: chain 'H' and resid 47 through 50 Processing sheet with id=31, first strand: chain 'H' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA H 98 " --> pdb=" O ILE H 91 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA H 169 " --> pdb=" O ARG H 176 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'I' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 26 through 27 current: chain 'I' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 66 through 73 current: chain 'I' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 124 through 136 current: chain 'I' and resid 157 through 164 Processing sheet with id=34, first strand: chain 'I' and resid 47 through 50 Processing sheet with id=35, first strand: chain 'I' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA I 98 " --> pdb=" O ILE I 91 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA I 169 " --> pdb=" O ARG I 176 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'J' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 26 through 27 current: chain 'J' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 73 current: chain 'J' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 124 through 136 current: chain 'J' and resid 157 through 164 Processing sheet with id=38, first strand: chain 'J' and resid 47 through 50 Processing sheet with id=39, first strand: chain 'J' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA J 98 " --> pdb=" O ILE J 91 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'J' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA J 169 " --> pdb=" O ARG J 176 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 26 through 27 current: chain 'K' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 66 through 73 current: chain 'K' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 124 through 136 current: chain 'K' and resid 157 through 164 Processing sheet with id=42, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=43, first strand: chain 'K' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA K 98 " --> pdb=" O ILE K 91 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'K' and resid 166 through 171 removed outlier: 5.356A pdb=" N ALA K 169 " --> pdb=" O ARG K 176 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'L' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 26 through 27 current: chain 'L' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 73 current: chain 'L' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 124 through 136 current: chain 'L' and resid 157 through 164 Processing sheet with id=46, first strand: chain 'L' and resid 47 through 50 Processing sheet with id=47, first strand: chain 'L' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA L 98 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'L' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA L 169 " --> pdb=" O ARG L 176 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'M' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 26 through 27 current: chain 'M' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 66 through 73 current: chain 'M' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 124 through 136 current: chain 'M' and resid 157 through 164 Processing sheet with id=50, first strand: chain 'M' and resid 47 through 50 Processing sheet with id=51, first strand: chain 'M' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA M 98 " --> pdb=" O ILE M 91 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'M' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA M 169 " --> pdb=" O ARG M 176 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'N' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 26 through 27 current: chain 'N' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 66 through 73 current: chain 'N' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 124 through 136 current: chain 'N' and resid 157 through 164 Processing sheet with id=54, first strand: chain 'N' and resid 47 through 50 Processing sheet with id=55, first strand: chain 'N' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA N 98 " --> pdb=" O ILE N 91 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'N' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA N 169 " --> pdb=" O ARG N 176 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'O' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 26 through 27 current: chain 'O' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 66 through 73 current: chain 'O' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 124 through 136 current: chain 'O' and resid 157 through 164 Processing sheet with id=58, first strand: chain 'O' and resid 47 through 50 Processing sheet with id=59, first strand: chain 'O' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA O 98 " --> pdb=" O ILE O 91 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'O' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA O 169 " --> pdb=" O ARG O 176 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'P' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 26 through 27 current: chain 'P' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 66 through 73 current: chain 'P' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 124 through 136 current: chain 'P' and resid 157 through 164 Processing sheet with id=62, first strand: chain 'P' and resid 47 through 50 Processing sheet with id=63, first strand: chain 'P' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA P 98 " --> pdb=" O ILE P 91 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'P' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA P 169 " --> pdb=" O ARG P 176 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'Q' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 26 through 27 current: chain 'Q' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 66 through 73 current: chain 'Q' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 124 through 136 current: chain 'Q' and resid 157 through 164 Processing sheet with id=66, first strand: chain 'Q' and resid 47 through 50 Processing sheet with id=67, first strand: chain 'Q' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA Q 98 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'Q' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA Q 169 " --> pdb=" O ARG Q 176 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'R' and resid 10 through 23 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 26 through 27 current: chain 'R' and resid 66 through 73 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 66 through 73 current: chain 'R' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 124 through 136 current: chain 'R' and resid 157 through 164 Processing sheet with id=70, first strand: chain 'R' and resid 47 through 50 Processing sheet with id=71, first strand: chain 'R' and resid 88 through 91 removed outlier: 4.017A pdb=" N ALA R 98 " --> pdb=" O ILE R 91 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'R' and resid 166 through 171 removed outlier: 5.357A pdb=" N ALA R 169 " --> pdb=" O ARG R 176 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1188 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: 4.54 Time building geometry restraints manager: 2.49 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: 9180 1.34 - 1.46: 6469 1.46 - 1.58: 13385 1.58 - 1.69: 0 1.69 - 1.81: 234 Bond restraints: 29268 Sorted by residual: bond pdb=" C ASP M 120 " pdb=" N PRO M 121 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 3.92e-01 bond pdb=" C ASP P 120 " pdb=" N PRO P 121 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 3.92e-01 bond pdb=" C ASP N 120 " pdb=" N PRO N 121 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.83e-01 bond pdb=" C ASP Q 120 " pdb=" N PRO Q 121 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.83e-01 bond pdb=" C ASP E 120 " pdb=" N PRO E 121 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.71e-01 ... (remaining 29263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 39194 1.06 - 2.13: 262 2.13 - 3.19: 198 3.19 - 4.25: 36 4.25 - 5.32: 18 Bond angle restraints: 39708 Sorted by residual: angle pdb=" N PHE O 14 " pdb=" CA PHE O 14 " pdb=" C PHE O 14 " ideal model delta sigma weight residual 108.46 110.49 -2.03 1.51e+00 4.39e-01 1.80e+00 angle pdb=" N PHE R 14 " pdb=" CA PHE R 14 " pdb=" C PHE R 14 " ideal model delta sigma weight residual 108.46 110.49 -2.03 1.51e+00 4.39e-01 1.80e+00 angle pdb=" N PHE B 14 " pdb=" CA PHE B 14 " pdb=" C PHE B 14 " ideal model delta sigma weight residual 108.46 110.48 -2.02 1.51e+00 4.39e-01 1.79e+00 angle pdb=" N PHE E 14 " pdb=" CA PHE E 14 " pdb=" C PHE E 14 " ideal model delta sigma weight residual 108.46 110.48 -2.02 1.51e+00 4.39e-01 1.79e+00 angle pdb=" N PHE Q 14 " pdb=" CA PHE Q 14 " pdb=" C PHE Q 14 " ideal model delta sigma weight residual 108.46 110.47 -2.01 1.51e+00 4.39e-01 1.78e+00 ... (remaining 39703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 15308 11.96 - 23.92: 1414 23.92 - 35.89: 378 35.89 - 47.85: 72 47.85 - 59.81: 54 Dihedral angle restraints: 17226 sinusoidal: 6552 harmonic: 10674 Sorted by residual: dihedral pdb=" CB MET E 39 " pdb=" CG MET E 39 " pdb=" SD MET E 39 " pdb=" CE MET E 39 " ideal model delta sinusoidal sigma weight residual 180.00 120.19 59.81 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET B 39 " pdb=" CG MET B 39 " pdb=" SD MET B 39 " pdb=" CE MET B 39 " ideal model delta sinusoidal sigma weight residual 180.00 120.19 59.81 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET K 39 " pdb=" CG MET K 39 " pdb=" SD MET K 39 " pdb=" CE MET K 39 " ideal model delta sinusoidal sigma weight residual 180.00 120.21 59.79 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 17223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2730 0.025 - 0.050: 893 0.050 - 0.075: 391 0.075 - 0.100: 176 0.100 - 0.125: 292 Chirality restraints: 4482 Sorted by residual: chirality pdb=" CA ILE Q 77 " pdb=" N ILE Q 77 " pdb=" C ILE Q 77 " pdb=" CB ILE Q 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE N 77 " pdb=" N ILE N 77 " pdb=" C ILE N 77 " pdb=" CB ILE N 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE E 77 " pdb=" N ILE E 77 " pdb=" C ILE E 77 " pdb=" CB ILE E 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 4479 not shown) Planarity restraints: 5130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 77 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.76e-01 pdb=" N PRO C 78 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO C 78 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 78 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 77 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.76e-01 pdb=" N PRO F 78 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO F 78 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO F 78 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 77 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.76e-01 pdb=" N PRO M 78 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO M 78 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO M 78 " -0.012 5.00e-02 4.00e+02 ... (remaining 5127 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 9938 2.85 - 3.36: 24014 3.36 - 3.87: 49998 3.87 - 4.39: 56184 4.39 - 4.90: 98107 Nonbonded interactions: 238241 Sorted by model distance: nonbonded pdb=" O ASP B 197 " pdb=" OG1 THR B 201 " model vdw 2.334 3.040 nonbonded pdb=" O ASP M 197 " pdb=" OG1 THR M 201 " model vdw 2.334 3.040 nonbonded pdb=" O ASP P 197 " pdb=" OG1 THR P 201 " model vdw 2.334 3.040 nonbonded pdb=" O ASP J 197 " pdb=" OG1 THR J 201 " model vdw 2.334 3.040 nonbonded pdb=" O ASP G 197 " pdb=" OG1 THR G 201 " model vdw 2.334 3.040 ... (remaining 238236 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 21.550 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 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 0.016 29268 Z= 0.090 Angle : 0.391 5.318 39708 Z= 0.206 Chirality : 0.042 0.125 4482 Planarity : 0.002 0.022 5130 Dihedral : 10.607 59.810 10494 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3744 helix: 1.17 (0.28), residues: 324 sheet: 0.44 (0.14), residues: 1530 loop : -0.79 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 16 TYR 0.004 0.001 TYR L 132 PHE 0.005 0.001 PHE E 178 TRP 0.001 0.000 TRP P 116 HIS 0.001 0.000 HIS Q 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.09 (29268) covalent geometry : angle 0.39101 / 0.21 (39708) hydrogen bonds : bond 0.28081 / 19.09 ( 450) hydrogen bonds : angle 7.99185 / 5.49 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1006 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9344 (p90) cc_final: 0.9136 (p90) REVERT: A 164 GLN cc_start: 0.7000 (mt0) cc_final: 0.6775 (mt0) REVERT: B 164 GLN cc_start: 0.7141 (mt0) cc_final: 0.6852 (mm-40) REVERT: C 127 ARG cc_start: 0.8763 (ttt180) cc_final: 0.8490 (ttt180) REVERT: C 164 GLN cc_start: 0.7010 (mt0) cc_final: 0.6769 (mt0) REVERT: D 164 GLN cc_start: 0.6994 (mt0) cc_final: 0.6770 (mt0) REVERT: E 164 GLN cc_start: 0.7140 (mt0) cc_final: 0.6850 (mm-40) REVERT: F 127 ARG cc_start: 0.8760 (ttt180) cc_final: 0.8490 (ttt180) REVERT: F 164 GLN cc_start: 0.7010 (mt0) cc_final: 0.6761 (mt0) REVERT: G 125 LYS cc_start: 0.8473 (mttt) cc_final: 0.8230 (mttp) REVERT: H 118 ASP cc_start: 0.7977 (m-30) cc_final: 0.7667 (m-30) REVERT: H 125 LYS cc_start: 0.8535 (mttt) cc_final: 0.8244 (mttp) REVERT: H 151 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7658 (mp0) REVERT: H 189 ASP cc_start: 0.7367 (p0) cc_final: 0.7146 (p0) REVERT: I 125 LYS cc_start: 0.8513 (mttt) cc_final: 0.8232 (mttp) REVERT: J 125 LYS cc_start: 0.8464 (mttt) cc_final: 0.8222 (mttp) REVERT: K 118 ASP cc_start: 0.7974 (m-30) cc_final: 0.7667 (m-30) REVERT: K 125 LYS cc_start: 0.8527 (mttt) cc_final: 0.8236 (mttp) REVERT: K 151 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7653 (mp0) REVERT: K 189 ASP cc_start: 0.7364 (p0) cc_final: 0.7145 (p0) REVERT: L 125 LYS cc_start: 0.8515 (mttt) cc_final: 0.8233 (mttp) REVERT: M 54 MET cc_start: 0.7918 (ptm) cc_final: 0.7462 (ptp) REVERT: M 61 LYS cc_start: 0.7671 (tptt) cc_final: 0.6895 (tttt) REVERT: M 186 THR cc_start: 0.8430 (m) cc_final: 0.8032 (p) REVERT: N 42 LYS cc_start: 0.8692 (mttt) cc_final: 0.8471 (mtmt) REVERT: N 54 MET cc_start: 0.7700 (ptm) cc_final: 0.7234 (ptp) REVERT: N 61 LYS cc_start: 0.7676 (tptt) cc_final: 0.6981 (tttt) REVERT: N 125 LYS cc_start: 0.8594 (mttt) cc_final: 0.8341 (mtmt) REVERT: N 143 ASN cc_start: 0.8785 (m-40) cc_final: 0.8561 (m-40) REVERT: N 147 ASP cc_start: 0.8532 (t0) cc_final: 0.8269 (t70) REVERT: N 164 GLN cc_start: 0.7556 (mt0) cc_final: 0.7319 (mt0) REVERT: N 186 THR cc_start: 0.8403 (m) cc_final: 0.8030 (p) REVERT: O 54 MET cc_start: 0.7811 (ptm) cc_final: 0.7287 (ptp) REVERT: O 61 LYS cc_start: 0.7834 (tptt) cc_final: 0.7127 (tttt) REVERT: O 124 GLN cc_start: 0.8364 (tt0) cc_final: 0.7982 (tt0) REVERT: O 186 THR cc_start: 0.8336 (m) cc_final: 0.7783 (p) REVERT: P 54 MET cc_start: 0.7917 (ptm) cc_final: 0.7465 (ptp) REVERT: P 61 LYS cc_start: 0.7673 (tptt) cc_final: 0.6896 (tttt) REVERT: P 186 THR cc_start: 0.8432 (m) cc_final: 0.8036 (p) REVERT: Q 42 LYS cc_start: 0.8694 (mttt) cc_final: 0.8470 (mtmt) REVERT: Q 54 MET cc_start: 0.7698 (ptm) cc_final: 0.7235 (ptp) REVERT: Q 61 LYS cc_start: 0.7682 (tptt) cc_final: 0.6985 (tttt) REVERT: Q 125 LYS cc_start: 0.8588 (mttt) cc_final: 0.8334 (mtmt) REVERT: Q 143 ASN cc_start: 0.8778 (m-40) cc_final: 0.8550 (m-40) REVERT: Q 147 ASP cc_start: 0.8537 (t0) cc_final: 0.8272 (t70) REVERT: Q 164 GLN cc_start: 0.7552 (mt0) cc_final: 0.7317 (mt0) REVERT: Q 186 THR cc_start: 0.8403 (m) cc_final: 0.8033 (p) REVERT: R 54 MET cc_start: 0.7815 (ptm) cc_final: 0.7289 (ptp) REVERT: R 61 LYS cc_start: 0.7827 (tptt) cc_final: 0.7123 (tttt) REVERT: R 124 GLN cc_start: 0.8366 (tt0) cc_final: 0.7982 (tt0) REVERT: R 156 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7798 (tt0) REVERT: R 186 THR cc_start: 0.8329 (m) cc_final: 0.7773 (p) outliers start: 0 outliers final: 0 residues processed: 1006 average time/residue: 0.1942 time to fit residues: 303.7083 Evaluate side-chains 676 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 676 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.3980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 GLN C 115 GLN E 124 GLN F 115 GLN G 164 GLN G 191 GLN H 164 GLN J 164 GLN J 191 GLN K 115 GLN K 164 GLN M 143 ASN N 115 GLN N 191 GLN O 115 GLN P 143 ASN Q 115 GLN Q 191 GLN R 115 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.090201 restraints weight = 40131.432| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.73 r_work: 0.2822 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 29268 Z= 0.177 Angle : 0.503 7.832 39708 Z= 0.257 Chirality : 0.045 0.158 4482 Planarity : 0.004 0.067 5130 Dihedral : 3.393 13.686 4014 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.60 % Allowed : 14.78 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3744 helix: 1.81 (0.31), residues: 324 sheet: 0.60 (0.15), residues: 1296 loop : -1.06 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 37 TYR 0.017 0.002 TYR E 193 PHE 0.018 0.001 PHE P 81 TRP 0.005 0.001 TRP D 116 HIS 0.003 0.001 HIS J 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (29268) covalent geometry : angle 0.50318 / 0.26 (39708) hydrogen bonds : bond 0.04431 / 3.00 ( 450) hydrogen bonds : angle 5.75669 / 4.00 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 657 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 151 GLU cc_start: 0.6399 (tp30) cc_final: 0.5879 (tp30) REVERT: A 164 GLN cc_start: 0.7016 (mt0) cc_final: 0.6579 (mm-40) REVERT: B 71 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9074 (tp) REVERT: B 164 GLN cc_start: 0.7164 (mt0) cc_final: 0.6706 (mm-40) REVERT: C 104 SER cc_start: 0.8799 (p) cc_final: 0.8515 (p) REVERT: D 26 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8349 (p) REVERT: D 151 GLU cc_start: 0.6400 (tp30) cc_final: 0.5861 (tp30) REVERT: D 164 GLN cc_start: 0.7014 (mt0) cc_final: 0.6587 (mm-40) REVERT: E 71 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9073 (tp) REVERT: E 164 GLN cc_start: 0.7134 (mt0) cc_final: 0.6694 (mm-40) REVERT: F 104 SER cc_start: 0.8797 (p) cc_final: 0.8513 (p) REVERT: H 44 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7435 (mt-10) REVERT: H 118 ASP cc_start: 0.8090 (m-30) cc_final: 0.7553 (m-30) REVERT: H 151 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7687 (mp0) REVERT: I 193 TYR cc_start: 0.8331 (t80) cc_final: 0.8046 (t80) REVERT: K 44 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7424 (mt-10) REVERT: K 118 ASP cc_start: 0.8075 (m-30) cc_final: 0.7544 (m-30) REVERT: L 193 TYR cc_start: 0.8343 (t80) cc_final: 0.8057 (t80) REVERT: M 54 MET cc_start: 0.7873 (ptm) cc_final: 0.7307 (ptp) REVERT: M 119 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: M 147 ASP cc_start: 0.8628 (t70) cc_final: 0.8286 (t70) REVERT: M 164 GLN cc_start: 0.7897 (mt0) cc_final: 0.7480 (mt0) REVERT: M 186 THR cc_start: 0.8455 (m) cc_final: 0.8017 (p) REVERT: N 54 MET cc_start: 0.7869 (ptm) cc_final: 0.7187 (ptp) REVERT: N 164 GLN cc_start: 0.7538 (mt0) cc_final: 0.7171 (mt0) REVERT: N 186 THR cc_start: 0.8400 (m) cc_final: 0.7989 (p) REVERT: N 198 GLN cc_start: 0.8826 (tt0) cc_final: 0.8601 (tt0) REVERT: O 54 MET cc_start: 0.7925 (ptm) cc_final: 0.7293 (ptp) REVERT: O 186 THR cc_start: 0.8339 (m) cc_final: 0.7866 (p) REVERT: O 198 GLN cc_start: 0.8659 (tt0) cc_final: 0.8336 (tt0) REVERT: P 54 MET cc_start: 0.7884 (ptm) cc_final: 0.7313 (ptp) REVERT: P 119 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: P 147 ASP cc_start: 0.8633 (t70) cc_final: 0.8296 (t70) REVERT: P 164 GLN cc_start: 0.7900 (mt0) cc_final: 0.7479 (mt0) REVERT: P 186 THR cc_start: 0.8443 (m) cc_final: 0.8001 (p) REVERT: Q 54 MET cc_start: 0.7851 (ptm) cc_final: 0.7157 (ptp) REVERT: Q 164 GLN cc_start: 0.7546 (mt0) cc_final: 0.7184 (mt0) REVERT: Q 186 THR cc_start: 0.8410 (m) cc_final: 0.8012 (p) REVERT: Q 198 GLN cc_start: 0.8816 (tt0) cc_final: 0.8584 (tt0) REVERT: R 54 MET cc_start: 0.7934 (ptm) cc_final: 0.7304 (ptp) REVERT: R 156 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7858 (tt0) REVERT: R 186 THR cc_start: 0.8332 (m) cc_final: 0.7848 (p) REVERT: R 198 GLN cc_start: 0.8673 (tt0) cc_final: 0.8347 (tt0) outliers start: 109 outliers final: 75 residues processed: 696 average time/residue: 0.1577 time to fit residues: 185.5842 Evaluate side-chains 676 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 595 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 85 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 80 ASP Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 180 GLU Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 85 CYS Chi-restraints excluded: chain Q residue 151 GLU Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 180 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [210, 253, 136, 120, 72, 243, 331, 270, 116, 362, 259] chunk 210 optimal weight: 0.6980 chunk 253 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN F 115 GLN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN O 124 GLN R 124 GLN R 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.090188 restraints weight = 40436.064| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.72 r_work: 0.2826 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29268 Z= 0.139 Angle : 0.472 8.481 39708 Z= 0.237 Chirality : 0.045 0.174 4482 Planarity : 0.004 0.067 5130 Dihedral : 3.437 14.938 4014 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.77 % Allowed : 16.50 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3744 helix: 1.78 (0.30), residues: 324 sheet: 0.60 (0.15), residues: 1296 loop : -1.16 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 127 TYR 0.027 0.001 TYR P 200 PHE 0.036 0.001 PHE Q 81 TRP 0.003 0.001 TRP N 116 HIS 0.002 0.001 HIS G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (29268) covalent geometry : angle 0.47190 / 0.24 (39708) hydrogen bonds : bond 0.03269 / 2.23 ( 450) hydrogen bonds : angle 5.22657 / 3.64 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 573 time to evaluate : 0.808 Fit side-chains REVERT: B 71 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9084 (tp) REVERT: B 118 ASP cc_start: 0.8022 (m-30) cc_final: 0.7298 (m-30) REVERT: B 164 GLN cc_start: 0.7152 (mt0) cc_final: 0.6716 (mm-40) REVERT: C 104 SER cc_start: 0.8714 (p) cc_final: 0.8452 (p) REVERT: C 200 TYR cc_start: 0.8586 (m-80) cc_final: 0.8363 (m-80) REVERT: E 71 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9083 (tp) REVERT: E 118 ASP cc_start: 0.8054 (m-30) cc_final: 0.7350 (m-30) REVERT: E 164 GLN cc_start: 0.7125 (mt0) cc_final: 0.6712 (mm-40) REVERT: F 104 SER cc_start: 0.8714 (p) cc_final: 0.8450 (p) REVERT: F 200 TYR cc_start: 0.8579 (m-80) cc_final: 0.8352 (m-80) REVERT: H 44 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7450 (mt-10) REVERT: H 118 ASP cc_start: 0.8069 (m-30) cc_final: 0.7521 (m-30) REVERT: H 151 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7726 (mp0) REVERT: I 193 TYR cc_start: 0.8303 (t80) cc_final: 0.8016 (t80) REVERT: K 44 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7439 (mt-10) REVERT: K 118 ASP cc_start: 0.8049 (m-30) cc_final: 0.7511 (m-30) REVERT: L 193 TYR cc_start: 0.8309 (t80) cc_final: 0.8020 (t80) REVERT: M 54 MET cc_start: 0.7768 (ptm) cc_final: 0.7383 (ptp) REVERT: M 186 THR cc_start: 0.8427 (m) cc_final: 0.8044 (p) REVERT: N 54 MET cc_start: 0.7870 (ptm) cc_final: 0.7205 (ptp) REVERT: N 125 LYS cc_start: 0.8579 (mttt) cc_final: 0.8306 (mttm) REVERT: N 164 GLN cc_start: 0.7488 (mt0) cc_final: 0.7138 (mt0) REVERT: N 186 THR cc_start: 0.8430 (m) cc_final: 0.8024 (p) REVERT: O 54 MET cc_start: 0.7832 (ptm) cc_final: 0.7226 (ptp) REVERT: O 119 GLU cc_start: 0.7740 (pt0) cc_final: 0.7420 (pt0) REVERT: O 125 LYS cc_start: 0.8651 (mttt) cc_final: 0.8332 (mttt) REVERT: O 186 THR cc_start: 0.8387 (m) cc_final: 0.8010 (p) REVERT: P 54 MET cc_start: 0.7772 (ptm) cc_final: 0.7389 (ptp) REVERT: P 186 THR cc_start: 0.8418 (m) cc_final: 0.8030 (p) REVERT: Q 54 MET cc_start: 0.7852 (ptm) cc_final: 0.7176 (ptp) REVERT: Q 125 LYS cc_start: 0.8556 (mttt) cc_final: 0.8287 (mttm) REVERT: Q 164 GLN cc_start: 0.7502 (mt0) cc_final: 0.7153 (mt0) REVERT: Q 186 THR cc_start: 0.8436 (m) cc_final: 0.8038 (p) REVERT: R 54 MET cc_start: 0.7830 (ptm) cc_final: 0.7219 (ptp) REVERT: R 71 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9026 (tp) REVERT: R 119 GLU cc_start: 0.7726 (pt0) cc_final: 0.7403 (pt0) REVERT: R 125 LYS cc_start: 0.8654 (mttt) cc_final: 0.8336 (mttt) REVERT: R 156 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7879 (tt0) REVERT: R 186 THR cc_start: 0.8384 (m) cc_final: 0.7999 (p) REVERT: R 198 GLN cc_start: 0.8853 (tt0) cc_final: 0.8649 (tt0) outliers start: 114 outliers final: 70 residues processed: 627 average time/residue: 0.1506 time to fit residues: 161.0606 Evaluate side-chains 641 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 568 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 151 GLU Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [197, 373, 276, 324, 23, 91, 209, 13, 311, 204, 278] chunk 197 optimal weight: 2.9990 chunk 373 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 278 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.088457 restraints weight = 40731.375| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.72 r_work: 0.2816 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 29268 Z= 0.187 Angle : 0.495 8.849 39708 Z= 0.250 Chirality : 0.045 0.136 4482 Planarity : 0.004 0.072 5130 Dihedral : 3.677 14.418 4014 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.96 % Allowed : 15.74 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3744 helix: 1.57 (0.30), residues: 324 sheet: 0.55 (0.15), residues: 1296 loop : -1.25 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 127 TYR 0.019 0.002 TYR M 200 PHE 0.027 0.001 PHE Q 81 TRP 0.003 0.001 TRP Q 116 HIS 0.003 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (29268) covalent geometry : angle 0.49515 / 0.25 (39708) hydrogen bonds : bond 0.03399 / 2.32 ( 450) hydrogen bonds : angle 5.21764 / 3.63 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 559 time to evaluate : 0.985 Fit side-chains REVERT: A 198 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 71 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9119 (tp) REVERT: B 118 ASP cc_start: 0.8110 (m-30) cc_final: 0.7414 (m-30) REVERT: D 198 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 71 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9119 (tp) REVERT: E 118 ASP cc_start: 0.8129 (m-30) cc_final: 0.7434 (m-30) REVERT: H 44 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 118 ASP cc_start: 0.8144 (m-30) cc_final: 0.7846 (m-30) REVERT: K 44 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7412 (mt-10) REVERT: K 118 ASP cc_start: 0.8126 (m-30) cc_final: 0.7826 (m-30) REVERT: M 54 MET cc_start: 0.7879 (ptm) cc_final: 0.7339 (ptp) REVERT: M 119 GLU cc_start: 0.7636 (pt0) cc_final: 0.7320 (pt0) REVERT: M 186 THR cc_start: 0.8486 (m) cc_final: 0.8152 (p) REVERT: N 54 MET cc_start: 0.7663 (ptm) cc_final: 0.7110 (ptp) REVERT: N 125 LYS cc_start: 0.8631 (mttt) cc_final: 0.8367 (mttp) REVERT: N 164 GLN cc_start: 0.7600 (mt0) cc_final: 0.7239 (mt0) REVERT: N 186 THR cc_start: 0.8464 (m) cc_final: 0.8064 (p) REVERT: O 54 MET cc_start: 0.7837 (ptm) cc_final: 0.7225 (ptp) REVERT: O 119 GLU cc_start: 0.7668 (pt0) cc_final: 0.7398 (pt0) REVERT: O 125 LYS cc_start: 0.8701 (mttt) cc_final: 0.8402 (mttt) REVERT: O 186 THR cc_start: 0.8421 (m) cc_final: 0.8064 (p) REVERT: O 198 GLN cc_start: 0.8632 (tt0) cc_final: 0.8424 (tt0) REVERT: P 54 MET cc_start: 0.7891 (ptm) cc_final: 0.7358 (ptp) REVERT: P 119 GLU cc_start: 0.7639 (pt0) cc_final: 0.7312 (pt0) REVERT: P 186 THR cc_start: 0.8475 (m) cc_final: 0.8138 (p) REVERT: Q 54 MET cc_start: 0.7658 (ptm) cc_final: 0.7107 (ptp) REVERT: Q 125 LYS cc_start: 0.8616 (mttt) cc_final: 0.8352 (mttp) REVERT: Q 164 GLN cc_start: 0.7598 (mt0) cc_final: 0.7242 (mt0) REVERT: Q 186 THR cc_start: 0.8468 (m) cc_final: 0.8073 (p) REVERT: R 54 MET cc_start: 0.7839 (ptm) cc_final: 0.7229 (ptp) REVERT: R 119 GLU cc_start: 0.7648 (pt0) cc_final: 0.7375 (pt0) REVERT: R 125 LYS cc_start: 0.8703 (mttt) cc_final: 0.8400 (mttt) REVERT: R 186 THR cc_start: 0.8423 (m) cc_final: 0.8054 (p) REVERT: R 198 GLN cc_start: 0.8826 (tt0) cc_final: 0.8507 (tt0) outliers start: 150 outliers final: 98 residues processed: 638 average time/residue: 0.1523 time to fit residues: 166.6753 Evaluate side-chains 629 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 529 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [366, 34, 122, 19, 281, 231, 87, 186, 159, 143, 319] chunk 366 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 319 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN M 115 GLN N 191 GLN P 115 GLN Q 191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.087891 restraints weight = 40884.944| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.72 r_work: 0.2792 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29268 Z= 0.211 Angle : 0.510 9.338 39708 Z= 0.257 Chirality : 0.046 0.145 4482 Planarity : 0.004 0.076 5130 Dihedral : 3.875 15.203 4014 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.29 % Allowed : 16.30 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3744 helix: 1.32 (0.30), residues: 324 sheet: 0.49 (0.15), residues: 1296 loop : -1.33 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 127 TYR 0.020 0.002 TYR P 200 PHE 0.022 0.001 PHE N 81 TRP 0.004 0.001 TRP O 116 HIS 0.003 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (29268) covalent geometry : angle 0.51041 / 0.26 (39708) hydrogen bonds : bond 0.03489 / 2.37 ( 450) hydrogen bonds : angle 5.27626 / 3.67 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 535 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9095 (tp) REVERT: B 118 ASP cc_start: 0.8109 (m-30) cc_final: 0.7390 (m-30) REVERT: E 71 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9090 (tp) REVERT: E 118 ASP cc_start: 0.8128 (m-30) cc_final: 0.7415 (m-30) REVERT: G 44 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7508 (mt-10) REVERT: G 66 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7807 (p) REVERT: G 118 ASP cc_start: 0.8288 (m-30) cc_final: 0.7864 (m-30) REVERT: H 118 ASP cc_start: 0.8163 (m-30) cc_final: 0.7835 (m-30) REVERT: I 18 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8971 (tt) REVERT: J 118 ASP cc_start: 0.8266 (m-30) cc_final: 0.7829 (m-30) REVERT: K 118 ASP cc_start: 0.8117 (m-30) cc_final: 0.7790 (m-30) REVERT: M 47 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (pt) REVERT: M 54 MET cc_start: 0.7711 (ptm) cc_final: 0.7113 (ptp) REVERT: M 119 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: M 186 THR cc_start: 0.8534 (m) cc_final: 0.8218 (p) REVERT: N 54 MET cc_start: 0.7730 (ptm) cc_final: 0.7139 (ptp) REVERT: N 125 LYS cc_start: 0.8625 (mttt) cc_final: 0.8345 (mtmt) REVERT: N 164 GLN cc_start: 0.7564 (mt0) cc_final: 0.7277 (mt0) REVERT: N 186 THR cc_start: 0.8494 (m) cc_final: 0.8148 (p) REVERT: O 54 MET cc_start: 0.7581 (ptm) cc_final: 0.7009 (ptp) REVERT: O 186 THR cc_start: 0.8433 (m) cc_final: 0.8075 (p) REVERT: P 47 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8533 (pt) REVERT: P 54 MET cc_start: 0.7729 (ptm) cc_final: 0.7135 (ptp) REVERT: P 119 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: P 186 THR cc_start: 0.8522 (m) cc_final: 0.8198 (p) REVERT: P 198 GLN cc_start: 0.8986 (tt0) cc_final: 0.8774 (tt0) REVERT: Q 54 MET cc_start: 0.7731 (ptm) cc_final: 0.7141 (ptp) REVERT: Q 125 LYS cc_start: 0.8612 (mttt) cc_final: 0.8330 (mtmt) REVERT: Q 164 GLN cc_start: 0.7576 (mt0) cc_final: 0.7286 (mt0) REVERT: Q 186 THR cc_start: 0.8489 (m) cc_final: 0.8153 (p) REVERT: R 54 MET cc_start: 0.7591 (ptm) cc_final: 0.7020 (ptp) REVERT: R 156 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: R 186 THR cc_start: 0.8446 (m) cc_final: 0.8091 (p) REVERT: R 198 GLN cc_start: 0.8774 (tt0) cc_final: 0.8511 (tt0) outliers start: 160 outliers final: 116 residues processed: 624 average time/residue: 0.1511 time to fit residues: 161.2924 Evaluate side-chains 648 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 523 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 80 ASP Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [2, 304, 5, 194, 125, 364, 33, 10, 241, 41, 222] chunk 2 optimal weight: 0.7980 chunk 304 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.090100 restraints weight = 40202.761| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.83 r_work: 0.2824 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29268 Z= 0.106 Angle : 0.450 8.592 39708 Z= 0.222 Chirality : 0.044 0.148 4482 Planarity : 0.004 0.079 5130 Dihedral : 3.461 14.641 4014 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.13 % Allowed : 17.39 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3744 helix: 1.50 (0.31), residues: 324 sheet: 0.52 (0.15), residues: 1296 loop : -1.24 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 127 TYR 0.020 0.001 TYR M 200 PHE 0.016 0.001 PHE N 81 TRP 0.004 0.001 TRP N 116 HIS 0.002 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (29268) covalent geometry : angle 0.44956 / 0.22 (39708) hydrogen bonds : bond 0.02497 / 1.71 ( 450) hydrogen bonds : angle 4.89549 / 3.43 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 559 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9105 (tp) REVERT: B 118 ASP cc_start: 0.8143 (m-30) cc_final: 0.7438 (m-30) REVERT: B 164 GLN cc_start: 0.7103 (mt0) cc_final: 0.6657 (mm-40) REVERT: E 71 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9107 (tp) REVERT: E 118 ASP cc_start: 0.8159 (m-30) cc_final: 0.7460 (m-30) REVERT: E 164 GLN cc_start: 0.7101 (mt0) cc_final: 0.6668 (mm-40) REVERT: H 48 THR cc_start: 0.8977 (m) cc_final: 0.8772 (p) REVERT: I 118 ASP cc_start: 0.8063 (m-30) cc_final: 0.7719 (m-30) REVERT: K 118 ASP cc_start: 0.8064 (m-30) cc_final: 0.7809 (m-30) REVERT: L 118 ASP cc_start: 0.8099 (m-30) cc_final: 0.7758 (m-30) REVERT: M 54 MET cc_start: 0.7786 (ptm) cc_final: 0.7193 (ptp) REVERT: M 186 THR cc_start: 0.8480 (m) cc_final: 0.8221 (p) REVERT: N 54 MET cc_start: 0.7748 (ptm) cc_final: 0.7174 (ptp) REVERT: N 125 LYS cc_start: 0.8569 (mttt) cc_final: 0.8356 (mttt) REVERT: N 164 GLN cc_start: 0.7476 (mt0) cc_final: 0.7081 (mm-40) REVERT: N 186 THR cc_start: 0.8470 (m) cc_final: 0.8145 (p) REVERT: O 54 MET cc_start: 0.7677 (ptm) cc_final: 0.7098 (ptp) REVERT: O 186 THR cc_start: 0.8409 (m) cc_final: 0.8062 (p) REVERT: P 54 MET cc_start: 0.7798 (ptm) cc_final: 0.7208 (ptp) REVERT: P 186 THR cc_start: 0.8475 (m) cc_final: 0.8208 (p) REVERT: Q 54 MET cc_start: 0.7752 (ptm) cc_final: 0.7173 (ptp) REVERT: Q 125 LYS cc_start: 0.8554 (mttt) cc_final: 0.8339 (mttt) REVERT: Q 164 GLN cc_start: 0.7479 (mt0) cc_final: 0.7088 (mm-40) REVERT: Q 186 THR cc_start: 0.8478 (m) cc_final: 0.8159 (p) REVERT: R 54 MET cc_start: 0.7684 (ptm) cc_final: 0.7105 (ptp) REVERT: R 156 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: R 186 THR cc_start: 0.8402 (m) cc_final: 0.8049 (p) REVERT: R 198 GLN cc_start: 0.8793 (tt0) cc_final: 0.8531 (tt0) outliers start: 125 outliers final: 96 residues processed: 629 average time/residue: 0.1510 time to fit residues: 162.7293 Evaluate side-chains 645 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 546 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 85 CYS Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 164 GLN Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 85 CYS Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 164 GLN Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [230, 259, 114, 138, 61, 139, 140, 33, 50, 45, 328] chunk 230 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 328 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 191 GLN Q 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.089398 restraints weight = 40421.750| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.76 r_work: 0.2828 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29268 Z= 0.126 Angle : 0.457 8.315 39708 Z= 0.228 Chirality : 0.044 0.144 4482 Planarity : 0.004 0.082 5130 Dihedral : 3.510 15.105 4014 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.40 % Allowed : 17.86 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3744 helix: 1.37 (0.30), residues: 324 sheet: 0.53 (0.15), residues: 1296 loop : -1.18 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 127 TYR 0.020 0.001 TYR P 200 PHE 0.015 0.001 PHE N 81 TRP 0.004 0.001 TRP D 116 HIS 0.002 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (29268) covalent geometry : angle 0.45665 / 0.23 (39708) hydrogen bonds : bond 0.02666 / 1.84 ( 450) hydrogen bonds : angle 4.86277 / 3.41 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 546 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9097 (tp) REVERT: B 118 ASP cc_start: 0.8072 (m-30) cc_final: 0.7356 (m-30) REVERT: E 71 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9095 (tp) REVERT: E 118 ASP cc_start: 0.8116 (m-30) cc_final: 0.7412 (m-30) REVERT: G 44 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7556 (mt-10) REVERT: H 48 THR cc_start: 0.8967 (m) cc_final: 0.8745 (p) REVERT: H 119 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8022 (mp0) REVERT: I 118 ASP cc_start: 0.8016 (m-30) cc_final: 0.7673 (m-30) REVERT: K 119 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8000 (mp0) REVERT: L 118 ASP cc_start: 0.8042 (m-30) cc_final: 0.7679 (m-30) REVERT: M 54 MET cc_start: 0.7799 (ptm) cc_final: 0.7138 (ptp) REVERT: M 186 THR cc_start: 0.8432 (m) cc_final: 0.8169 (p) REVERT: N 54 MET cc_start: 0.7771 (ptm) cc_final: 0.7180 (ptp) REVERT: N 125 LYS cc_start: 0.8574 (mttt) cc_final: 0.8315 (mtmt) REVERT: N 164 GLN cc_start: 0.7469 (mt0) cc_final: 0.7088 (mm-40) REVERT: N 186 THR cc_start: 0.8450 (m) cc_final: 0.8110 (p) REVERT: O 54 MET cc_start: 0.7464 (ptm) cc_final: 0.6891 (ptp) REVERT: O 66 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8237 (p) REVERT: O 186 THR cc_start: 0.8388 (m) cc_final: 0.8039 (p) REVERT: P 44 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8205 (tt0) REVERT: P 54 MET cc_start: 0.7820 (ptm) cc_final: 0.7164 (ptp) REVERT: P 186 THR cc_start: 0.8428 (m) cc_final: 0.8173 (p) REVERT: Q 54 MET cc_start: 0.7768 (ptm) cc_final: 0.7177 (ptp) REVERT: Q 125 LYS cc_start: 0.8572 (mttt) cc_final: 0.8303 (mtmt) REVERT: Q 164 GLN cc_start: 0.7491 (mt0) cc_final: 0.7100 (mm-40) REVERT: Q 186 THR cc_start: 0.8447 (m) cc_final: 0.8116 (p) REVERT: R 54 MET cc_start: 0.7460 (ptm) cc_final: 0.6885 (ptp) REVERT: R 66 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8225 (p) REVERT: R 156 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: R 186 THR cc_start: 0.8391 (m) cc_final: 0.8033 (p) REVERT: R 198 GLN cc_start: 0.8780 (tt0) cc_final: 0.8510 (tt0) outliers start: 133 outliers final: 110 residues processed: 624 average time/residue: 0.1497 time to fit residues: 160.5500 Evaluate side-chains 644 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 529 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 85 CYS Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 85 CYS Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [95, 187, 29, 226, 288, 355, 263, 346, 93, 228, 74] chunk 95 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 355 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 346 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN I 45 GLN L 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.088425 restraints weight = 40625.295| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.78 r_work: 0.2810 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29268 Z= 0.157 Angle : 0.473 8.222 39708 Z= 0.238 Chirality : 0.044 0.147 4482 Planarity : 0.004 0.085 5130 Dihedral : 3.664 16.006 4014 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.53 % Allowed : 17.86 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3744 helix: 1.32 (0.30), residues: 324 sheet: 0.48 (0.15), residues: 1296 loop : -1.19 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 127 TYR 0.018 0.001 TYR M 200 PHE 0.025 0.001 PHE O 81 TRP 0.005 0.001 TRP D 116 HIS 0.002 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (29268) covalent geometry : angle 0.47338 / 0.24 (39708) hydrogen bonds : bond 0.02905 / 2.00 ( 450) hydrogen bonds : angle 5.00944 / 3.54 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 539 time to evaluate : 1.032 Fit side-chains REVERT: B 71 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9112 (tp) REVERT: B 118 ASP cc_start: 0.8081 (m-30) cc_final: 0.7362 (m-30) REVERT: E 71 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9112 (tp) REVERT: E 118 ASP cc_start: 0.8114 (m-30) cc_final: 0.7403 (m-30) REVERT: H 48 THR cc_start: 0.8979 (m) cc_final: 0.8725 (p) REVERT: H 119 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8060 (mp0) REVERT: H 130 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9117 (mt) REVERT: I 118 ASP cc_start: 0.8083 (m-30) cc_final: 0.7713 (m-30) REVERT: K 119 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8069 (mp0) REVERT: K 130 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9123 (mt) REVERT: L 118 ASP cc_start: 0.8072 (m-30) cc_final: 0.7714 (m-30) REVERT: M 44 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8202 (tt0) REVERT: M 54 MET cc_start: 0.7759 (ptm) cc_final: 0.7131 (ptp) REVERT: M 186 THR cc_start: 0.8473 (m) cc_final: 0.8182 (p) REVERT: N 54 MET cc_start: 0.7768 (ptm) cc_final: 0.7172 (ptp) REVERT: N 164 GLN cc_start: 0.7495 (mt0) cc_final: 0.7095 (mm-40) REVERT: N 186 THR cc_start: 0.8498 (m) cc_final: 0.8115 (p) REVERT: O 54 MET cc_start: 0.7543 (ptm) cc_final: 0.6909 (ptp) REVERT: O 66 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8207 (p) REVERT: O 119 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: O 125 LYS cc_start: 0.8704 (mttt) cc_final: 0.8413 (mttt) REVERT: O 186 THR cc_start: 0.8430 (m) cc_final: 0.8065 (p) REVERT: P 54 MET cc_start: 0.7770 (ptm) cc_final: 0.7143 (ptp) REVERT: P 186 THR cc_start: 0.8468 (m) cc_final: 0.8185 (p) REVERT: Q 54 MET cc_start: 0.7766 (ptm) cc_final: 0.7166 (ptp) REVERT: Q 164 GLN cc_start: 0.7513 (mt0) cc_final: 0.7113 (mm-40) REVERT: Q 186 THR cc_start: 0.8488 (m) cc_final: 0.8104 (p) REVERT: R 54 MET cc_start: 0.7540 (ptm) cc_final: 0.6902 (ptp) REVERT: R 66 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8190 (p) REVERT: R 119 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: R 125 LYS cc_start: 0.8704 (mttt) cc_final: 0.8424 (mttt) REVERT: R 156 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: R 186 THR cc_start: 0.8422 (m) cc_final: 0.8047 (p) REVERT: R 198 GLN cc_start: 0.8758 (tt0) cc_final: 0.8539 (tt0) outliers start: 137 outliers final: 110 residues processed: 619 average time/residue: 0.1537 time to fit residues: 163.1353 Evaluate side-chains 650 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 531 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 85 CYS Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 164 GLN Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 85 CYS Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 151 GLU Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 164 GLN Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [41, 39, 182, 37, 206, 50, 131, 143, 19, 204, 369] chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 206 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.089984 restraints weight = 40436.984| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.75 r_work: 0.2839 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29268 Z= 0.113 Angle : 0.451 7.809 39708 Z= 0.225 Chirality : 0.044 0.145 4482 Planarity : 0.004 0.086 5130 Dihedral : 3.500 15.868 4014 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.23 % Allowed : 18.25 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3744 helix: 1.38 (0.31), residues: 324 sheet: 0.49 (0.15), residues: 1296 loop : -1.15 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 127 TYR 0.023 0.001 TYR M 200 PHE 0.025 0.001 PHE O 81 TRP 0.004 0.001 TRP D 116 HIS 0.002 0.001 HIS K 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 (29268) covalent geometry : angle 0.45125 / 0.23 (39708) hydrogen bonds : bond 0.02452 / 1.69 ( 450) hydrogen bonds : angle 4.87157 / 3.45 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 557 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.6195 (tp30) cc_final: 0.4564 (pt0) REVERT: B 71 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9141 (tp) REVERT: B 118 ASP cc_start: 0.8041 (m-30) cc_final: 0.7314 (m-30) REVERT: C 124 GLN cc_start: 0.8488 (tt0) cc_final: 0.8167 (tt0) REVERT: D 151 GLU cc_start: 0.6206 (tp30) cc_final: 0.4559 (pt0) REVERT: E 71 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9131 (tp) REVERT: E 118 ASP cc_start: 0.8072 (m-30) cc_final: 0.7357 (m-30) REVERT: H 119 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7927 (mp0) REVERT: H 130 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9124 (mt) REVERT: I 118 ASP cc_start: 0.7987 (m-30) cc_final: 0.7678 (m-30) REVERT: K 119 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7925 (mp0) REVERT: K 130 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9130 (mt) REVERT: L 118 ASP cc_start: 0.8028 (m-30) cc_final: 0.7703 (m-30) REVERT: M 54 MET cc_start: 0.7710 (ptm) cc_final: 0.7130 (ptp) REVERT: M 66 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8323 (p) REVERT: M 186 THR cc_start: 0.8404 (m) cc_final: 0.8125 (p) REVERT: N 54 MET cc_start: 0.7741 (ptm) cc_final: 0.7299 (ptp) REVERT: N 125 LYS cc_start: 0.8544 (mttt) cc_final: 0.8287 (mtmt) REVERT: N 164 GLN cc_start: 0.7404 (mt0) cc_final: 0.7145 (mt0) REVERT: N 186 THR cc_start: 0.8470 (m) cc_final: 0.8071 (p) REVERT: O 54 MET cc_start: 0.7542 (ptm) cc_final: 0.6933 (ptp) REVERT: O 66 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8205 (p) REVERT: O 186 THR cc_start: 0.8418 (m) cc_final: 0.8071 (p) REVERT: P 54 MET cc_start: 0.7718 (ptm) cc_final: 0.7138 (ptp) REVERT: P 186 THR cc_start: 0.8405 (m) cc_final: 0.8137 (p) REVERT: Q 54 MET cc_start: 0.7733 (ptm) cc_final: 0.7282 (ptp) REVERT: Q 125 LYS cc_start: 0.8534 (mttt) cc_final: 0.8267 (mtmt) REVERT: Q 164 GLN cc_start: 0.7405 (mt0) cc_final: 0.7146 (mt0) REVERT: Q 186 THR cc_start: 0.8470 (m) cc_final: 0.8065 (p) REVERT: R 54 MET cc_start: 0.7532 (ptm) cc_final: 0.6909 (ptp) REVERT: R 66 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8195 (p) REVERT: R 156 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: R 186 THR cc_start: 0.8414 (m) cc_final: 0.8059 (p) outliers start: 128 outliers final: 112 residues processed: 632 average time/residue: 0.1554 time to fit residues: 168.6674 Evaluate side-chains 656 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 536 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 85 CYS Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 206 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 164 GLN Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 85 CYS Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 151 GLU Chi-restraints excluded: chain Q residue 180 GLU Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain Q residue 206 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 164 GLN Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [11, 275, 235, 257, 138, 9, 19, 359, 157, 210, 74] chunk 11 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 257 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 359 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 74 optimal weight: 0.0770 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 129 GLN F 129 GLN R 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.091868 restraints weight = 40031.396| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.75 r_work: 0.2871 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29268 Z= 0.085 Angle : 0.440 6.945 39708 Z= 0.220 Chirality : 0.044 0.156 4482 Planarity : 0.004 0.081 5130 Dihedral : 3.296 15.850 4014 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.47 % Allowed : 19.05 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3744 helix: 1.45 (0.31), residues: 324 sheet: 0.57 (0.16), residues: 1296 loop : -1.15 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 127 TYR 0.024 0.001 TYR D 145 PHE 0.039 0.001 PHE N 81 TRP 0.004 0.001 TRP D 116 HIS 0.002 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (29268) covalent geometry : angle 0.43986 / 0.22 (39708) hydrogen bonds : bond 0.02085 / 1.45 ( 450) hydrogen bonds : angle 4.73764 / 3.37 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 561 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.6158 (tp30) cc_final: 0.4628 (pt0) REVERT: A 164 GLN cc_start: 0.7051 (mt0) cc_final: 0.6610 (mm-40) REVERT: B 71 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9148 (tp) REVERT: B 118 ASP cc_start: 0.8022 (m-30) cc_final: 0.7290 (m-30) REVERT: B 164 GLN cc_start: 0.7080 (mt0) cc_final: 0.6625 (mm-40) REVERT: C 164 GLN cc_start: 0.7059 (mt0) cc_final: 0.6666 (mm-40) REVERT: D 151 GLU cc_start: 0.6139 (tp30) cc_final: 0.4610 (pt0) REVERT: D 164 GLN cc_start: 0.7045 (mt0) cc_final: 0.6598 (mm-40) REVERT: E 71 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9140 (tp) REVERT: E 118 ASP cc_start: 0.8041 (m-30) cc_final: 0.7331 (m-30) REVERT: E 164 GLN cc_start: 0.7073 (mt0) cc_final: 0.6615 (mm-40) REVERT: F 164 GLN cc_start: 0.7064 (mt0) cc_final: 0.6657 (mm-40) REVERT: H 119 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7980 (mp0) REVERT: H 130 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9122 (mt) REVERT: I 118 ASP cc_start: 0.7984 (m-30) cc_final: 0.7661 (m-30) REVERT: K 119 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7954 (mp0) REVERT: K 130 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9124 (mt) REVERT: L 118 ASP cc_start: 0.8062 (m-30) cc_final: 0.7728 (m-30) REVERT: M 54 MET cc_start: 0.7745 (ptm) cc_final: 0.7142 (ptp) REVERT: M 186 THR cc_start: 0.8345 (m) cc_final: 0.8086 (p) REVERT: N 54 MET cc_start: 0.7819 (ptm) cc_final: 0.7332 (ptp) REVERT: N 125 LYS cc_start: 0.8534 (mttt) cc_final: 0.8276 (mtmt) REVERT: N 186 THR cc_start: 0.8431 (m) cc_final: 0.8054 (p) REVERT: O 54 MET cc_start: 0.7491 (ptm) cc_final: 0.6874 (ptp) REVERT: O 186 THR cc_start: 0.8396 (m) cc_final: 0.8029 (p) REVERT: P 54 MET cc_start: 0.7743 (ptm) cc_final: 0.7143 (ptp) REVERT: P 186 THR cc_start: 0.8350 (m) cc_final: 0.8112 (p) REVERT: Q 54 MET cc_start: 0.7806 (ptm) cc_final: 0.7309 (ptp) REVERT: Q 125 LYS cc_start: 0.8513 (mttt) cc_final: 0.8249 (mtmt) REVERT: Q 186 THR cc_start: 0.8425 (m) cc_final: 0.8050 (p) REVERT: R 54 MET cc_start: 0.7489 (ptm) cc_final: 0.6872 (ptp) REVERT: R 66 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8189 (p) REVERT: R 144 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: R 156 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: R 186 THR cc_start: 0.8411 (m) cc_final: 0.8040 (p) outliers start: 105 outliers final: 92 residues processed: 625 average time/residue: 0.1515 time to fit residues: 162.7331 Evaluate side-chains 641 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 542 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 85 CYS Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 206 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 180 GLU Chi-restraints excluded: chain O residue 197 ASP Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 164 GLN Chi-restraints excluded: chain P residue 197 ASP Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 85 CYS Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 151 GLU Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain Q residue 206 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 197 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [275, 35, 53, 3, 241, 285, 120, 107, 258, 323, 293] chunk 275 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN F 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.106366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.089563 restraints weight = 39836.467| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.82 r_work: 0.2803 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 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 : 0.004 0.039 29268 Z= 0.178 Angle : 0.487 7.268 39708 Z= 0.248 Chirality : 0.045 0.153 4482 Planarity : 0.004 0.083 5130 Dihedral : 3.692 16.417 4014 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 19.01 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3744 helix: 1.25 (0.30), residues: 324 sheet: 0.51 (0.16), residues: 1296 loop : -1.18 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 127 TYR 0.026 0.002 TYR P 200 PHE 0.040 0.001 PHE Q 81 TRP 0.009 0.001 TRP C 116 HIS 0.002 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (29268) covalent geometry : angle 0.48694 / 0.25 (39708) hydrogen bonds : bond 0.02991 / 2.05 ( 450) hydrogen bonds : angle 4.95270 / 3.50 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6424.52 seconds wall clock time: 110 minutes 49.76 seconds (6649.76 seconds total)