Starting phenix.real_space_refine on Tue Aug 26 04:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btq_44895/08_2025/9btq_44895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btq_44895/08_2025/9btq_44895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btq_44895/08_2025/9btq_44895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btq_44895/08_2025/9btq_44895.map" model { file = "/net/cci-nas-00/data/ceres_data/9btq_44895/08_2025/9btq_44895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btq_44895/08_2025/9btq_44895.cif" } resolution = 2.4 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 ------------------------------------------------------------------------------- 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= 0.112 sd= 0.875 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: 3 Type Number sf(0) Gaussians C 21480 2.51 5 N 5800 2.21 5 O 7160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34440 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 861 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Restraints were copied for chains: C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, A, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d Time building chain proxies: 2.59, per 1000 atoms: 0.08 Number of scatterers: 34440 At special positions: 0 Unit cell: (116.63, 116.63, 241.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 7160 8.00 N 5800 7.00 C 21480 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9040 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 160 sheets defined 29.0% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.653A pdb=" N GLY B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 153 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.655A pdb=" N GLY D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 153 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 Processing helix chain 'F' and resid 94 through 98 Processing helix chain 'F' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 153 Processing helix chain 'H' and resid 94 through 98 Processing helix chain 'H' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 153 Processing helix chain 'I' and resid 94 through 98 Processing helix chain 'I' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 153 Processing helix chain 'J' and resid 94 through 98 Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY J 137 " --> pdb=" O LYS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 153 Processing helix chain 'K' and resid 94 through 98 Processing helix chain 'K' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY K 137 " --> pdb=" O LYS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 153 Processing helix chain 'L' and resid 94 through 98 Processing helix chain 'L' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 153 Processing helix chain 'M' and resid 94 through 98 Processing helix chain 'M' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 153 Processing helix chain 'N' and resid 94 through 98 Processing helix chain 'N' and resid 122 through 137 removed outlier: 3.655A pdb=" N GLY N 137 " --> pdb=" O LYS N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 153 Processing helix chain 'O' and resid 94 through 98 Processing helix chain 'O' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY O 137 " --> pdb=" O LYS O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 153 Processing helix chain 'P' and resid 94 through 98 Processing helix chain 'P' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY P 137 " --> pdb=" O LYS P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 153 Processing helix chain 'Q' and resid 94 through 98 Processing helix chain 'Q' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY Q 137 " --> pdb=" O LYS Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 153 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY R 137 " --> pdb=" O LYS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 153 Processing helix chain 'S' and resid 94 through 98 Processing helix chain 'S' and resid 122 through 137 removed outlier: 3.653A pdb=" N GLY S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 153 Processing helix chain 'T' and resid 94 through 98 Processing helix chain 'T' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY T 137 " --> pdb=" O LYS T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 153 Processing helix chain 'U' and resid 94 through 98 Processing helix chain 'U' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY U 137 " --> pdb=" O LYS U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 153 Processing helix chain 'V' and resid 94 through 98 Processing helix chain 'V' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY V 137 " --> pdb=" O LYS V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 139 through 153 Processing helix chain 'W' and resid 94 through 98 Processing helix chain 'W' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY W 137 " --> pdb=" O LYS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 153 Processing helix chain 'X' and resid 94 through 98 Processing helix chain 'X' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY X 137 " --> pdb=" O LYS X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 139 through 153 Processing helix chain 'Y' and resid 94 through 98 Processing helix chain 'Y' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY Y 137 " --> pdb=" O LYS Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 153 Processing helix chain 'Z' and resid 94 through 98 Processing helix chain 'Z' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY Z 137 " --> pdb=" O LYS Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 139 through 153 Processing helix chain '0' and resid 94 through 98 Processing helix chain '0' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 0 137 " --> pdb=" O LYS 0 133 " (cutoff:3.500A) Processing helix chain '0' and resid 139 through 153 Processing helix chain '1' and resid 94 through 98 Processing helix chain '1' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 1 137 " --> pdb=" O LYS 1 133 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 153 Processing helix chain '2' and resid 94 through 98 Processing helix chain '2' and resid 122 through 137 removed outlier: 3.653A pdb=" N GLY 2 137 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) Processing helix chain '2' and resid 139 through 153 Processing helix chain '3' and resid 94 through 98 Processing helix chain '3' and resid 122 through 137 removed outlier: 3.653A pdb=" N GLY 3 137 " --> pdb=" O LYS 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 139 through 153 Processing helix chain '4' and resid 94 through 98 Processing helix chain '4' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 4 137 " --> pdb=" O LYS 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 139 through 153 Processing helix chain '5' and resid 94 through 98 Processing helix chain '5' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 5 137 " --> pdb=" O LYS 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 139 through 153 Processing helix chain '6' and resid 94 through 98 Processing helix chain '6' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 6 137 " --> pdb=" O LYS 6 133 " (cutoff:3.500A) Processing helix chain '6' and resid 139 through 153 Processing helix chain '7' and resid 94 through 98 Processing helix chain '7' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 7 137 " --> pdb=" O LYS 7 133 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 153 Processing helix chain '8' and resid 94 through 98 Processing helix chain '8' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 8 137 " --> pdb=" O LYS 8 133 " (cutoff:3.500A) Processing helix chain '8' and resid 139 through 153 Processing helix chain '9' and resid 94 through 98 Processing helix chain '9' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY 9 137 " --> pdb=" O LYS 9 133 " (cutoff:3.500A) Processing helix chain '9' and resid 139 through 153 Processing helix chain 'a' and resid 94 through 98 Processing helix chain 'a' and resid 122 through 137 removed outlier: 3.653A pdb=" N GLY a 137 " --> pdb=" O LYS a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 153 Processing helix chain 'b' and resid 94 through 98 Processing helix chain 'b' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY b 137 " --> pdb=" O LYS b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 153 Processing helix chain 'c' and resid 94 through 98 Processing helix chain 'c' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY c 137 " --> pdb=" O LYS c 133 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 153 Processing helix chain 'd' and resid 94 through 98 Processing helix chain 'd' and resid 122 through 137 removed outlier: 3.654A pdb=" N GLY d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 153 Processing sheet with id=1, first strand: chain 'A' and resid 43 through 53 Processing sheet with id=2, first strand: chain 'A' and resid 74 through 76 Processing sheet with id=3, first strand: chain 'A' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA A 106 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 87 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 104 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=5, first strand: chain 'B' and resid 43 through 53 Processing sheet with id=6, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=7, first strand: chain 'B' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA B 106 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 87 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE B 104 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=9, first strand: chain 'C' and resid 43 through 53 Processing sheet with id=10, first strand: chain 'C' and resid 74 through 76 Processing sheet with id=11, first strand: chain 'C' and resid 81 through 87 removed outlier: 3.787A pdb=" N ALA C 106 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA C 87 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 104 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=13, first strand: chain 'D' and resid 43 through 53 Processing sheet with id=14, first strand: chain 'D' and resid 74 through 76 Processing sheet with id=15, first strand: chain 'D' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA D 106 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA D 87 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 104 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=17, first strand: chain 'E' and resid 43 through 53 Processing sheet with id=18, first strand: chain 'E' and resid 74 through 76 Processing sheet with id=19, first strand: chain 'E' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA E 106 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 87 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE E 104 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=21, first strand: chain 'F' and resid 43 through 53 Processing sheet with id=22, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=23, first strand: chain 'F' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA F 106 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA F 87 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE F 104 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=25, first strand: chain 'G' and resid 43 through 53 Processing sheet with id=26, first strand: chain 'G' and resid 74 through 76 Processing sheet with id=27, first strand: chain 'G' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA G 106 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA G 87 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE G 104 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=29, first strand: chain 'H' and resid 43 through 53 Processing sheet with id=30, first strand: chain 'H' and resid 74 through 76 Processing sheet with id=31, first strand: chain 'H' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA H 106 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA H 87 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE H 104 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 91 through 92 Processing sheet with id=33, first strand: chain 'I' and resid 43 through 53 Processing sheet with id=34, first strand: chain 'I' and resid 74 through 76 Processing sheet with id=35, first strand: chain 'I' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA I 106 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA I 87 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE I 104 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 91 through 92 Processing sheet with id=37, first strand: chain 'J' and resid 43 through 53 Processing sheet with id=38, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=39, first strand: chain 'J' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA J 106 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA J 87 " --> pdb=" O ILE J 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE J 104 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=41, first strand: chain 'K' and resid 43 through 53 Processing sheet with id=42, first strand: chain 'K' and resid 74 through 76 Processing sheet with id=43, first strand: chain 'K' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA K 106 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA K 87 " --> pdb=" O ILE K 104 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE K 104 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'K' and resid 91 through 92 Processing sheet with id=45, first strand: chain 'L' and resid 43 through 53 Processing sheet with id=46, first strand: chain 'L' and resid 74 through 76 Processing sheet with id=47, first strand: chain 'L' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA L 106 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA L 87 " --> pdb=" O ILE L 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE L 104 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'L' and resid 91 through 92 Processing sheet with id=49, first strand: chain 'M' and resid 43 through 53 Processing sheet with id=50, first strand: chain 'M' and resid 74 through 76 Processing sheet with id=51, first strand: chain 'M' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA M 106 " --> pdb=" O SER M 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA M 87 " --> pdb=" O ILE M 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE M 104 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'M' and resid 91 through 92 Processing sheet with id=53, first strand: chain 'N' and resid 43 through 53 Processing sheet with id=54, first strand: chain 'N' and resid 74 through 76 Processing sheet with id=55, first strand: chain 'N' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA N 106 " --> pdb=" O SER N 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA N 87 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE N 104 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'N' and resid 91 through 92 Processing sheet with id=57, first strand: chain 'O' and resid 43 through 53 Processing sheet with id=58, first strand: chain 'O' and resid 74 through 76 Processing sheet with id=59, first strand: chain 'O' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA O 106 " --> pdb=" O SER O 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA O 87 " --> pdb=" O ILE O 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE O 104 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'O' and resid 91 through 92 Processing sheet with id=61, first strand: chain 'P' and resid 43 through 53 Processing sheet with id=62, first strand: chain 'P' and resid 74 through 76 Processing sheet with id=63, first strand: chain 'P' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA P 106 " --> pdb=" O SER P 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA P 87 " --> pdb=" O ILE P 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE P 104 " --> pdb=" O ALA P 87 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'P' and resid 91 through 92 Processing sheet with id=65, first strand: chain 'Q' and resid 43 through 53 Processing sheet with id=66, first strand: chain 'Q' and resid 74 through 76 Processing sheet with id=67, first strand: chain 'Q' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA Q 106 " --> pdb=" O SER Q 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA Q 87 " --> pdb=" O ILE Q 104 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE Q 104 " --> pdb=" O ALA Q 87 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'Q' and resid 91 through 92 Processing sheet with id=69, first strand: chain 'R' and resid 43 through 53 Processing sheet with id=70, first strand: chain 'R' and resid 74 through 76 Processing sheet with id=71, first strand: chain 'R' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA R 106 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA R 87 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE R 104 " --> pdb=" O ALA R 87 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'R' and resid 91 through 92 Processing sheet with id=73, first strand: chain 'S' and resid 43 through 53 Processing sheet with id=74, first strand: chain 'S' and resid 74 through 76 Processing sheet with id=75, first strand: chain 'S' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA S 106 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA S 87 " --> pdb=" O ILE S 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE S 104 " --> pdb=" O ALA S 87 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'S' and resid 91 through 92 Processing sheet with id=77, first strand: chain 'T' and resid 43 through 53 Processing sheet with id=78, first strand: chain 'T' and resid 74 through 76 Processing sheet with id=79, first strand: chain 'T' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA T 106 " --> pdb=" O SER T 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA T 87 " --> pdb=" O ILE T 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE T 104 " --> pdb=" O ALA T 87 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'T' and resid 91 through 92 Processing sheet with id=81, first strand: chain 'U' and resid 43 through 53 Processing sheet with id=82, first strand: chain 'U' and resid 74 through 76 Processing sheet with id=83, first strand: chain 'U' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA U 106 " --> pdb=" O SER U 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA U 87 " --> pdb=" O ILE U 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE U 104 " --> pdb=" O ALA U 87 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'U' and resid 91 through 92 Processing sheet with id=85, first strand: chain 'V' and resid 43 through 53 Processing sheet with id=86, first strand: chain 'V' and resid 74 through 76 Processing sheet with id=87, first strand: chain 'V' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA V 106 " --> pdb=" O SER V 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA V 87 " --> pdb=" O ILE V 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE V 104 " --> pdb=" O ALA V 87 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'V' and resid 91 through 92 Processing sheet with id=89, first strand: chain 'W' and resid 43 through 53 Processing sheet with id=90, first strand: chain 'W' and resid 74 through 76 Processing sheet with id=91, first strand: chain 'W' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA W 106 " --> pdb=" O SER W 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA W 87 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE W 104 " --> pdb=" O ALA W 87 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'W' and resid 91 through 92 Processing sheet with id=93, first strand: chain 'X' and resid 43 through 53 Processing sheet with id=94, first strand: chain 'X' and resid 74 through 76 Processing sheet with id=95, first strand: chain 'X' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA X 106 " --> pdb=" O SER X 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA X 87 " --> pdb=" O ILE X 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE X 104 " --> pdb=" O ALA X 87 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'X' and resid 91 through 92 Processing sheet with id=97, first strand: chain 'Y' and resid 43 through 53 Processing sheet with id=98, first strand: chain 'Y' and resid 74 through 76 Processing sheet with id=99, first strand: chain 'Y' and resid 81 through 87 removed outlier: 3.787A pdb=" N ALA Y 106 " --> pdb=" O SER Y 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA Y 87 " --> pdb=" O ILE Y 104 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE Y 104 " --> pdb=" O ALA Y 87 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'Y' and resid 91 through 92 Processing sheet with id=101, first strand: chain 'Z' and resid 43 through 53 Processing sheet with id=102, first strand: chain 'Z' and resid 74 through 76 Processing sheet with id=103, first strand: chain 'Z' and resid 81 through 87 removed outlier: 3.787A pdb=" N ALA Z 106 " --> pdb=" O SER Z 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA Z 87 " --> pdb=" O ILE Z 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE Z 104 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'Z' and resid 91 through 92 Processing sheet with id=105, first strand: chain '0' and resid 43 through 53 Processing sheet with id=106, first strand: chain '0' and resid 74 through 76 Processing sheet with id=107, first strand: chain '0' and resid 81 through 87 removed outlier: 3.787A pdb=" N ALA 0 106 " --> pdb=" O SER 0 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 0 87 " --> pdb=" O ILE 0 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 0 104 " --> pdb=" O ALA 0 87 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain '0' and resid 91 through 92 Processing sheet with id=109, first strand: chain '1' and resid 43 through 53 Processing sheet with id=110, first strand: chain '1' and resid 74 through 76 Processing sheet with id=111, first strand: chain '1' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 1 106 " --> pdb=" O SER 1 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 1 87 " --> pdb=" O ILE 1 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 1 104 " --> pdb=" O ALA 1 87 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain '1' and resid 91 through 92 Processing sheet with id=113, first strand: chain '2' and resid 43 through 53 Processing sheet with id=114, first strand: chain '2' and resid 74 through 76 Processing sheet with id=115, first strand: chain '2' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 2 106 " --> pdb=" O SER 2 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 2 87 " --> pdb=" O ILE 2 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 2 104 " --> pdb=" O ALA 2 87 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain '2' and resid 91 through 92 Processing sheet with id=117, first strand: chain '3' and resid 43 through 53 Processing sheet with id=118, first strand: chain '3' and resid 74 through 76 Processing sheet with id=119, first strand: chain '3' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 3 106 " --> pdb=" O SER 3 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 3 87 " --> pdb=" O ILE 3 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 3 104 " --> pdb=" O ALA 3 87 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain '3' and resid 91 through 92 Processing sheet with id=121, first strand: chain '4' and resid 43 through 53 Processing sheet with id=122, first strand: chain '4' and resid 74 through 76 Processing sheet with id=123, first strand: chain '4' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 4 106 " --> pdb=" O SER 4 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 4 87 " --> pdb=" O ILE 4 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 4 104 " --> pdb=" O ALA 4 87 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain '4' and resid 91 through 92 Processing sheet with id=125, first strand: chain '5' and resid 43 through 53 Processing sheet with id=126, first strand: chain '5' and resid 74 through 76 Processing sheet with id=127, first strand: chain '5' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 5 106 " --> pdb=" O SER 5 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 5 87 " --> pdb=" O ILE 5 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 5 104 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain '5' and resid 91 through 92 Processing sheet with id=129, first strand: chain '6' and resid 43 through 53 Processing sheet with id=130, first strand: chain '6' and resid 74 through 76 Processing sheet with id=131, first strand: chain '6' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 6 106 " --> pdb=" O SER 6 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 6 87 " --> pdb=" O ILE 6 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 6 104 " --> pdb=" O ALA 6 87 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain '6' and resid 91 through 92 Processing sheet with id=133, first strand: chain '7' and resid 43 through 53 Processing sheet with id=134, first strand: chain '7' and resid 74 through 76 Processing sheet with id=135, first strand: chain '7' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 7 106 " --> pdb=" O SER 7 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 7 87 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 7 104 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) Processing sheet with id=136, first strand: chain '7' and resid 91 through 92 Processing sheet with id=137, first strand: chain '8' and resid 43 through 53 Processing sheet with id=138, first strand: chain '8' and resid 74 through 76 Processing sheet with id=139, first strand: chain '8' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA 8 106 " --> pdb=" O SER 8 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 8 87 " --> pdb=" O ILE 8 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 8 104 " --> pdb=" O ALA 8 87 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain '8' and resid 91 through 92 Processing sheet with id=141, first strand: chain '9' and resid 43 through 53 Processing sheet with id=142, first strand: chain '9' and resid 74 through 76 Processing sheet with id=143, first strand: chain '9' and resid 81 through 87 removed outlier: 3.787A pdb=" N ALA 9 106 " --> pdb=" O SER 9 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA 9 87 " --> pdb=" O ILE 9 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 9 104 " --> pdb=" O ALA 9 87 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain '9' and resid 91 through 92 Processing sheet with id=145, first strand: chain 'a' and resid 43 through 53 Processing sheet with id=146, first strand: chain 'a' and resid 74 through 76 Processing sheet with id=147, first strand: chain 'a' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA a 106 " --> pdb=" O SER a 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA a 87 " --> pdb=" O ILE a 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE a 104 " --> pdb=" O ALA a 87 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'a' and resid 91 through 92 Processing sheet with id=149, first strand: chain 'b' and resid 43 through 53 Processing sheet with id=150, first strand: chain 'b' and resid 74 through 76 Processing sheet with id=151, first strand: chain 'b' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA b 106 " --> pdb=" O SER b 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA b 87 " --> pdb=" O ILE b 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE b 104 " --> pdb=" O ALA b 87 " (cutoff:3.500A) Processing sheet with id=152, first strand: chain 'b' and resid 91 through 92 Processing sheet with id=153, first strand: chain 'c' and resid 43 through 53 Processing sheet with id=154, first strand: chain 'c' and resid 74 through 76 Processing sheet with id=155, first strand: chain 'c' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA c 106 " --> pdb=" O SER c 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA c 87 " --> pdb=" O ILE c 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE c 104 " --> pdb=" O ALA c 87 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'c' and resid 91 through 92 Processing sheet with id=157, first strand: chain 'd' and resid 43 through 53 Processing sheet with id=158, first strand: chain 'd' and resid 74 through 76 Processing sheet with id=159, first strand: chain 'd' and resid 81 through 87 removed outlier: 3.788A pdb=" N ALA d 106 " --> pdb=" O SER d 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA d 87 " --> pdb=" O ILE d 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE d 104 " --> pdb=" O ALA d 87 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'd' and resid 91 through 92 1720 hydrogen bonds defined for protein. 4680 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: 7.18 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 5880 1.29 - 1.35: 5680 1.35 - 1.42: 2480 1.42 - 1.48: 6079 1.48 - 1.55: 14721 Bond restraints: 34840 Sorted by residual: bond pdb=" CB GLU W 66 " pdb=" CG GLU W 66 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.48e-01 bond pdb=" CB GLU U 66 " pdb=" CG GLU U 66 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.46e-01 bond pdb=" CB GLU F 66 " pdb=" CG GLU F 66 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.45e-01 bond pdb=" CB GLU G 66 " pdb=" CG GLU G 66 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.40e-01 bond pdb=" CB GLU 6 66 " pdb=" CG GLU 6 66 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.35e-01 ... (remaining 34835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 45019 1.26 - 2.52: 2369 2.52 - 3.78: 212 3.78 - 5.04: 200 5.04 - 6.30: 40 Bond angle restraints: 47840 Sorted by residual: angle pdb=" C GLY a 137 " pdb=" N SER a 138 " pdb=" CA SER a 138 " ideal model delta sigma weight residual 122.08 126.10 -4.02 1.47e+00 4.63e-01 7.48e+00 angle pdb=" C GLY 1 137 " pdb=" N SER 1 138 " pdb=" CA SER 1 138 " ideal model delta sigma weight residual 122.08 126.09 -4.01 1.47e+00 4.63e-01 7.43e+00 angle pdb=" C GLY Q 137 " pdb=" N SER Q 138 " pdb=" CA SER Q 138 " ideal model delta sigma weight residual 122.08 126.08 -4.00 1.47e+00 4.63e-01 7.41e+00 angle pdb=" C GLY 0 137 " pdb=" N SER 0 138 " pdb=" CA SER 0 138 " ideal model delta sigma weight residual 122.08 126.08 -4.00 1.47e+00 4.63e-01 7.41e+00 angle pdb=" C GLY 2 137 " pdb=" N SER 2 138 " pdb=" CA SER 2 138 " ideal model delta sigma weight residual 122.08 126.08 -4.00 1.47e+00 4.63e-01 7.41e+00 ... (remaining 47835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 17640 14.97 - 29.94: 2040 29.94 - 44.91: 480 44.91 - 59.88: 120 59.88 - 74.85: 40 Dihedral angle restraints: 20320 sinusoidal: 6280 harmonic: 14040 Sorted by residual: dihedral pdb=" CA PRO S 70 " pdb=" C PRO S 70 " pdb=" N SER S 71 " pdb=" CA SER S 71 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PRO D 70 " pdb=" C PRO D 70 " pdb=" N SER D 71 " pdb=" CA SER D 71 " ideal model delta harmonic sigma weight residual 180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PRO Z 70 " pdb=" C PRO Z 70 " pdb=" N SER Z 71 " pdb=" CA SER Z 71 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 20317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3775 0.040 - 0.079: 1744 0.079 - 0.119: 609 0.119 - 0.158: 192 0.158 - 0.198: 40 Chirality restraints: 6360 Sorted by residual: chirality pdb=" CB THR B 110 " pdb=" CA THR B 110 " pdb=" OG1 THR B 110 " pdb=" CG2 THR B 110 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CB THR E 110 " pdb=" CA THR E 110 " pdb=" OG1 THR E 110 " pdb=" CG2 THR E 110 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB THR P 110 " pdb=" CA THR P 110 " pdb=" OG1 THR P 110 " pdb=" CG2 THR P 110 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 6357 not shown) Planarity restraints: 6080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP 4 129 " 0.004 2.00e-02 2.50e+03 8.62e-03 7.43e-01 pdb=" CG ASP 4 129 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASP 4 129 " 0.005 2.00e-02 2.50e+03 pdb=" OD2 ASP 4 129 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP T 129 " -0.004 2.00e-02 2.50e+03 8.56e-03 7.33e-01 pdb=" CG ASP T 129 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASP T 129 " -0.005 2.00e-02 2.50e+03 pdb=" OD2 ASP T 129 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Z 129 " -0.004 2.00e-02 2.50e+03 8.56e-03 7.32e-01 pdb=" CG ASP Z 129 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASP Z 129 " -0.005 2.00e-02 2.50e+03 pdb=" OD2 ASP Z 129 " -0.005 2.00e-02 2.50e+03 ... (remaining 6077 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 12872 2.86 - 3.37: 29011 3.37 - 3.88: 57930 3.88 - 4.39: 63978 4.39 - 4.90: 114115 Nonbonded interactions: 277906 Sorted by model distance: nonbonded pdb=" NH2 ARG 7 43 " pdb=" OE1 GLU 8 66 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG N 43 " pdb=" OE1 GLU O 66 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG T 43 " pdb=" OE1 GLU U 66 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG V 43 " pdb=" OE1 GLU W 66 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG H 43 " pdb=" OE1 GLU I 66 " model vdw 2.354 3.120 ... (remaining 277901 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: 0.14 Found NCS groups: ncs_group { reference = 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'A' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.260 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 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 : 0.006 0.032 34840 Z= 0.239 Angle : 0.666 6.302 47840 Z= 0.365 Chirality : 0.054 0.198 6360 Planarity : 0.004 0.026 6080 Dihedral : 14.866 74.851 11280 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.80 % Allowed : 18.05 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.11), residues: 4880 helix: 2.19 (0.15), residues: 1080 sheet: 0.81 (0.12), residues: 1760 loop : -1.44 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 1 125 TYR 0.006 0.002 TYR Y 86 PHE 0.006 0.002 PHE 2 63 TRP 0.011 0.003 TRP D 150 Details of bonding type rmsd covalent geometry : bond 0.00584 (34840) covalent geometry : angle 0.66648 (47840) hydrogen bonds : bond 0.20719 ( 1720) hydrogen bonds : angle 7.79560 ( 4680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 201 time to evaluate : 1.296 Fit side-chains REVERT: N 157 LEU cc_start: 0.9286 (mt) cc_final: 0.9055 (mp) REVERT: O 108 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8935 (mt-10) REVERT: 4 142 ASP cc_start: 0.8848 (m-30) cc_final: 0.8629 (m-30) outliers start: 211 outliers final: 67 residues processed: 412 average time/residue: 0.4248 time to fit residues: 229.4163 Evaluate side-chains 189 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 122 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 85 SER Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 85 SER Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 68 VAL Chi-restraints excluded: chain 3 residue 85 SER Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 68 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 6 residue 68 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 68 VAL Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN 0 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.048811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.046092 restraints weight = 112927.496| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.31 r_work: 0.2609 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 34840 Z= 0.216 Angle : 0.626 9.077 47840 Z= 0.344 Chirality : 0.052 0.161 6360 Planarity : 0.004 0.042 6080 Dihedral : 6.283 53.425 5227 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.68 % Allowed : 15.41 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.11), residues: 4880 helix: 2.12 (0.14), residues: 1160 sheet: 1.11 (0.12), residues: 1840 loop : -1.20 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 43 TYR 0.010 0.002 TYR Y 86 PHE 0.016 0.002 PHE W 35 TRP 0.015 0.002 TRP L 150 Details of bonding type rmsd covalent geometry : bond 0.00534 (34840) covalent geometry : angle 0.62573 (47840) hydrogen bonds : bond 0.04370 ( 1720) hydrogen bonds : angle 5.81390 ( 4680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 1.384 Fit side-chains REVERT: N 124 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: X 124 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8960 (tt0) REVERT: 4 142 ASP cc_start: 0.8878 (m-30) cc_final: 0.8636 (m-30) outliers start: 61 outliers final: 43 residues processed: 176 average time/residue: 0.6835 time to fit residues: 146.6762 Evaluate side-chains 164 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 124 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 41 GLN Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 376 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 294 optimal weight: 0.0070 chunk 105 optimal weight: 0.9980 chunk 286 optimal weight: 6.9990 chunk 456 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 444 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 410 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN a 41 GLN d 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.050189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.047460 restraints weight = 111712.535| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.31 r_work: 0.2649 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34840 Z= 0.116 Angle : 0.486 5.972 47840 Z= 0.265 Chirality : 0.047 0.147 6360 Planarity : 0.003 0.026 6080 Dihedral : 5.501 52.351 5192 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.43 % Allowed : 14.23 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.11), residues: 4880 helix: 2.68 (0.14), residues: 1160 sheet: 1.18 (0.12), residues: 1840 loop : -1.10 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 43 TYR 0.005 0.001 TYR K 86 PHE 0.009 0.001 PHE 3 76 TRP 0.009 0.001 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00270 (34840) covalent geometry : angle 0.48641 (47840) hydrogen bonds : bond 0.03377 ( 1720) hydrogen bonds : angle 5.30581 ( 4680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 1.290 Fit side-chains REVERT: S 124 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: X 124 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8916 (tt0) outliers start: 52 outliers final: 44 residues processed: 172 average time/residue: 0.6962 time to fit residues: 145.8243 Evaluate side-chains 168 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 41 GLN Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 437 optimal weight: 3.9990 chunk 174 optimal weight: 0.0980 chunk 213 optimal weight: 5.9990 chunk 337 optimal weight: 0.0870 chunk 445 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 overall best weight: 2.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.049849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.047116 restraints weight = 111459.070| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 1.31 r_work: 0.2638 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34840 Z= 0.139 Angle : 0.509 6.633 47840 Z= 0.278 Chirality : 0.048 0.152 6360 Planarity : 0.003 0.028 6080 Dihedral : 5.599 53.133 5192 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.57 % Allowed : 13.43 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.11), residues: 4880 helix: 2.62 (0.14), residues: 1160 sheet: 1.14 (0.12), residues: 1840 loop : -1.04 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 43 TYR 0.006 0.001 TYR X 86 PHE 0.011 0.001 PHE 3 76 TRP 0.011 0.001 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00332 (34840) covalent geometry : angle 0.50868 (47840) hydrogen bonds : bond 0.03551 ( 1720) hydrogen bonds : angle 5.38421 ( 4680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 1.617 Fit side-chains REVERT: S 124 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: X 124 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8904 (tt0) outliers start: 57 outliers final: 49 residues processed: 176 average time/residue: 0.7003 time to fit residues: 150.1384 Evaluate side-chains 174 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 142 ASP Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 41 GLN Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 224 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 362 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 339 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.048414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.045697 restraints weight = 112824.244| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 1.31 r_work: 0.2593 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 34840 Z= 0.276 Angle : 0.672 9.317 47840 Z= 0.371 Chirality : 0.054 0.166 6360 Planarity : 0.005 0.050 6080 Dihedral : 6.235 58.262 5191 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.12 % Allowed : 13.27 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.11), residues: 4880 helix: 1.98 (0.14), residues: 1160 sheet: 1.00 (0.11), residues: 1840 loop : -1.11 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 125 TYR 0.012 0.002 TYR Y 86 PHE 0.019 0.002 PHE R 76 TRP 0.018 0.003 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00693 (34840) covalent geometry : angle 0.67162 (47840) hydrogen bonds : bond 0.04713 ( 1720) hydrogen bonds : angle 5.84419 ( 4680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 118 time to evaluate : 1.363 Fit side-chains REVERT: N 124 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: S 124 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: T 100 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9006 (tp) REVERT: X 124 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8951 (tt0) REVERT: 2 100 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8847 (tp) outliers start: 77 outliers final: 56 residues processed: 180 average time/residue: 0.6481 time to fit residues: 143.7964 Evaluate side-chains 177 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 116 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 124 GLU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 100 LEU Chi-restraints excluded: chain T residue 101 THR Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 41 GLN Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 44 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 440 optimal weight: 8.9990 chunk 375 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 326 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 454 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.050046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.047311 restraints weight = 110538.195| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 1.31 r_work: 0.2643 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34840 Z= 0.122 Angle : 0.492 6.148 47840 Z= 0.267 Chirality : 0.047 0.147 6360 Planarity : 0.003 0.033 6080 Dihedral : 5.546 59.203 5191 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.48 % Allowed : 13.65 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.11), residues: 4880 helix: 2.52 (0.14), residues: 1160 sheet: 1.05 (0.11), residues: 1840 loop : -1.04 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 43 TYR 0.006 0.001 TYR X 86 PHE 0.009 0.001 PHE 3 76 TRP 0.010 0.001 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00287 (34840) covalent geometry : angle 0.49167 (47840) hydrogen bonds : bond 0.03355 ( 1720) hydrogen bonds : angle 5.30990 ( 4680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 1.413 Fit side-chains REVERT: S 124 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: X 124 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8905 (tt0) outliers start: 54 outliers final: 49 residues processed: 173 average time/residue: 0.6882 time to fit residues: 144.9750 Evaluate side-chains 173 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 142 ASP Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 32 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 262 optimal weight: 0.5980 chunk 379 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 430 optimal weight: 8.9990 chunk 415 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 391 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 451 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.049098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.046370 restraints weight = 112148.259| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 1.31 r_work: 0.2614 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34840 Z= 0.195 Angle : 0.575 7.846 47840 Z= 0.316 Chirality : 0.050 0.159 6360 Planarity : 0.004 0.040 6080 Dihedral : 5.903 58.990 5191 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.81 % Allowed : 13.43 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.11), residues: 4880 helix: 2.27 (0.14), residues: 1160 sheet: 1.00 (0.11), residues: 1840 loop : -1.06 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 125 TYR 0.009 0.002 TYR X 86 PHE 0.013 0.002 PHE R 76 TRP 0.016 0.002 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00482 (34840) covalent geometry : angle 0.57495 (47840) hydrogen bonds : bond 0.04038 ( 1720) hydrogen bonds : angle 5.58929 ( 4680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 120 time to evaluate : 1.331 Fit side-chains REVERT: O 66 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: S 124 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: X 124 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8944 (tt0) outliers start: 66 outliers final: 55 residues processed: 177 average time/residue: 0.6207 time to fit residues: 134.7890 Evaluate side-chains 178 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 101 THR Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 354 optimal weight: 10.0000 chunk 402 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 277 optimal weight: 0.7980 chunk 170 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.049393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.046655 restraints weight = 111662.196| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 1.31 r_work: 0.2623 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34840 Z= 0.173 Angle : 0.545 7.055 47840 Z= 0.299 Chirality : 0.049 0.154 6360 Planarity : 0.004 0.037 6080 Dihedral : 5.798 59.605 5191 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.81 % Allowed : 13.54 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.11), residues: 4880 helix: 2.29 (0.14), residues: 1160 sheet: 0.99 (0.11), residues: 1840 loop : -1.05 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 125 TYR 0.008 0.001 TYR X 86 PHE 0.012 0.001 PHE 3 76 TRP 0.015 0.002 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00422 (34840) covalent geometry : angle 0.54529 (47840) hydrogen bonds : bond 0.03818 ( 1720) hydrogen bonds : angle 5.49597 ( 4680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 120 time to evaluate : 1.213 Fit side-chains REVERT: N 124 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: S 124 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: X 124 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8931 (tt0) REVERT: 2 100 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8787 (tp) outliers start: 66 outliers final: 59 residues processed: 178 average time/residue: 0.5746 time to fit residues: 125.2757 Evaluate side-chains 183 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 120 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 124 GLU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 101 THR Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 180 optimal weight: 8.9990 chunk 466 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 317 optimal weight: 10.0000 chunk 402 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 449 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.048157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.045447 restraints weight = 112643.452| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 1.30 r_work: 0.2583 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 34840 Z= 0.338 Angle : 0.738 10.182 47840 Z= 0.410 Chirality : 0.058 0.180 6360 Planarity : 0.006 0.058 6080 Dihedral : 6.435 57.301 5191 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 13.63 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.11), residues: 4880 helix: 1.57 (0.14), residues: 1160 sheet: 0.88 (0.11), residues: 1840 loop : -1.04 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 9 148 TYR 0.015 0.002 TYR X 86 PHE 0.022 0.003 PHE R 76 TRP 0.031 0.003 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00852 (34840) covalent geometry : angle 0.73794 (47840) hydrogen bonds : bond 0.05128 ( 1720) hydrogen bonds : angle 5.95776 ( 4680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 1.375 Fit side-chains REVERT: N 124 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: S 124 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: X 124 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: 2 100 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8857 (tp) REVERT: b 124 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9096 (tt0) outliers start: 70 outliers final: 62 residues processed: 179 average time/residue: 0.5669 time to fit residues: 125.7541 Evaluate side-chains 182 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 115 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 124 GLU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 101 THR Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain b residue 124 GLU Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 136 optimal weight: 5.9990 chunk 453 optimal weight: 1.9990 chunk 462 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 373 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.049487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.046760 restraints weight = 111539.369| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 1.31 r_work: 0.2626 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34840 Z= 0.154 Angle : 0.531 6.861 47840 Z= 0.290 Chirality : 0.048 0.151 6360 Planarity : 0.004 0.042 6080 Dihedral : 5.807 59.795 5191 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.73 % Allowed : 13.74 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.11), residues: 4880 helix: 2.16 (0.14), residues: 1160 sheet: 0.92 (0.11), residues: 1840 loop : -0.99 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 43 TYR 0.008 0.001 TYR X 86 PHE 0.011 0.001 PHE R 76 TRP 0.019 0.002 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00371 (34840) covalent geometry : angle 0.53084 (47840) hydrogen bonds : bond 0.03677 ( 1720) hydrogen bonds : angle 5.46216 ( 4680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 1.269 Fit side-chains REVERT: S 124 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: X 124 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8908 (tt0) REVERT: b 124 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9048 (tt0) outliers start: 63 outliers final: 55 residues processed: 179 average time/residue: 0.6130 time to fit residues: 133.9999 Evaluate side-chains 182 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 101 THR Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 157 LEU Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 103 VAL Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 103 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 8 residue 103 VAL Chi-restraints excluded: chain 9 residue 103 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain b residue 124 GLU Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 330 optimal weight: 10.0000 chunk 412 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 452 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.048028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.045319 restraints weight = 112826.294| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 1.31 r_work: 0.2579 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 34840 Z= 0.360 Angle : 0.762 10.552 47840 Z= 0.424 Chirality : 0.060 0.196 6360 Planarity : 0.007 0.060 6080 Dihedral : 6.530 59.811 5191 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.90 % Allowed : 13.65 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.11), residues: 4880 helix: 1.41 (0.14), residues: 1160 sheet: 0.83 (0.11), residues: 1840 loop : -1.08 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 9 148 TYR 0.015 0.003 TYR X 86 PHE 0.024 0.003 PHE R 76 TRP 0.040 0.003 TRP W 150 Details of bonding type rmsd covalent geometry : bond 0.00911 (34840) covalent geometry : angle 0.76228 (47840) hydrogen bonds : bond 0.05305 ( 1720) hydrogen bonds : angle 6.00545 ( 4680) =============================================================================== Job complete usr+sys time: 8158.31 seconds wall clock time: 140 minutes 28.27 seconds (8428.27 seconds total)