Starting phenix.real_space_refine on Sat Jun 28 15:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btq_44895/06_2025/9btq_44895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btq_44895/06_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_44895/06_2025/9btq_44895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btq_44895/06_2025/9btq_44895.map" model { file = "/net/cci-nas-00/data/ceres_data/9btq_44895/06_2025/9btq_44895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btq_44895/06_2025/9btq_44895.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34440 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" 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: 0, 3, 2, 5, 4, 7, 6, 9, 8, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, d Time building chain proxies: 7.00, per 1000 atoms: 0.20 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: 7.90 Conformation dependent library (CDL) restraints added in 5.1 seconds 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: 5.26 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: 13.17 Time building geometry restraints manager: 9.59 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: 0.34 Found NCS groups: ncs_group { reference = chain '1' selection = chain '0' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 64.890 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.280 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:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (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 TRP 0.011 0.003 TRP D 150 PHE 0.006 0.002 PHE 2 63 TYR 0.006 0.002 TYR Y 86 ARG 0.002 0.000 ARG 1 125 Details of bonding type rmsd hydrogen bonds : bond 0.20719 ( 1720) hydrogen bonds : angle 7.79560 ( 4680) covalent geometry : bond 0.00584 (34840) covalent geometry : angle 0.66648 (47840) *********************** 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 : 3.474 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: 0.9680 time to fit residues: 522.6195 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 : 3.778 ------------------------------------------------------------------------------- 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 405 optimal weight: 1.9990 chunk 363 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 376 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 435 optimal weight: 7.9990 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 = 0.046097 restraints weight = 112319.683| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.31 r_work: 0.2609 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (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 TRP 0.015 0.002 TRP L 150 PHE 0.016 0.002 PHE W 35 TYR 0.010 0.002 TYR Y 86 ARG 0.006 0.001 ARG a 43 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 1720) hydrogen bonds : angle 5.81390 ( 4680) covalent geometry : bond 0.00534 (34840) covalent geometry : angle 0.62573 (47840) *********************** 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 : 3.640 Fit side-chains REVERT: N 124 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: X 124 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8957 (tt0) REVERT: 4 142 ASP cc_start: 0.8879 (m-30) cc_final: 0.8637 (m-30) outliers start: 61 outliers final: 43 residues processed: 176 average time/residue: 1.4183 time to fit residues: 306.5412 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 : 4.098 ------------------------------------------------------------------------------- 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 139 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 410 optimal weight: 4.9990 chunk 450 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 342 optimal weight: 0.5980 chunk 442 optimal weight: 5.9990 chunk 456 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 = 0.2754 r_free = 0.2754 target = 0.048973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.046253 restraints weight = 112356.035| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 1.31 r_work: 0.2610 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 34840 Z= 0.203 Angle : 0.594 8.296 47840 Z= 0.326 Chirality : 0.051 0.158 6360 Planarity : 0.004 0.038 6080 Dihedral : 6.028 58.625 5192 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.90 % Allowed : 13.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 4880 helix: 2.19 (0.14), residues: 1160 sheet: 1.07 (0.12), residues: 1840 loop : -1.15 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 150 PHE 0.015 0.002 PHE 3 76 TYR 0.008 0.002 TYR Y 86 ARG 0.004 0.001 ARG a 43 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 1720) hydrogen bonds : angle 5.68952 ( 4680) covalent geometry : bond 0.00500 (34840) covalent geometry : angle 0.59357 (47840) *********************** 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 187 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 118 time to evaluate : 3.439 Fit side-chains REVERT: J 66 GLU cc_start: 0.8785 (tt0) cc_final: 0.8575 (tt0) REVERT: S 124 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: X 124 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8943 (tt0) REVERT: 2 100 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8817 (tp) REVERT: 4 142 ASP cc_start: 0.8877 (m-30) cc_final: 0.8626 (m-30) REVERT: 9 108 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8965 (mt-10) outliers start: 69 outliers final: 51 residues processed: 173 average time/residue: 1.3710 time to fit residues: 291.4935 Evaluate side-chains 171 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 3.585 ------------------------------------------------------------------------------- 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 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 100 LEU 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 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 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 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 9 residue 108 GLU 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 282 optimal weight: 1.9990 chunk 458 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 445 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 440 optimal weight: 10.0000 chunk 409 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.048348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.045634 restraints weight = 112613.339| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 1.30 r_work: 0.2590 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 34840 Z= 0.275 Angle : 0.676 9.305 47840 Z= 0.373 Chirality : 0.055 0.165 6360 Planarity : 0.005 0.049 6080 Dihedral : 6.312 58.036 5192 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.28 % Allowed : 12.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 4880 helix: 1.77 (0.14), residues: 1160 sheet: 0.96 (0.11), residues: 1840 loop : -1.19 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP W 150 PHE 0.019 0.002 PHE R 76 TYR 0.012 0.002 TYR X 86 ARG 0.005 0.001 ARG R 125 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 1720) hydrogen bonds : angle 5.85495 ( 4680) covalent geometry : bond 0.00687 (34840) covalent geometry : angle 0.67625 (47840) *********************** 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 202 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 119 time to evaluate : 3.470 Fit side-chains REVERT: F 66 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: J 66 GLU cc_start: 0.8779 (tt0) cc_final: 0.8576 (tt0) REVERT: N 124 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: S 124 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: T 100 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9095 (tp) REVERT: X 124 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: 2 100 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8850 (tp) REVERT: 9 108 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8957 (mt-10) outliers start: 83 outliers final: 60 residues processed: 191 average time/residue: 1.2617 time to fit residues: 299.3882 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 : 3.428 ------------------------------------------------------------------------------- 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 68 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 66 GLU 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 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 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 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 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 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 9 residue 108 GLU 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 83 GLN 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 75 optimal weight: 5.9990 chunk 469 optimal weight: 9.9990 chunk 466 optimal weight: 3.9990 chunk 355 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 454 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 = 0.2765 r_free = 0.2765 target = 0.049354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.046630 restraints weight = 111814.352| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.30 r_work: 0.2620 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34840 Z= 0.167 Angle : 0.548 7.454 47840 Z= 0.299 Chirality : 0.049 0.152 6360 Planarity : 0.004 0.040 6080 Dihedral : 5.877 59.678 5192 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.84 % Allowed : 13.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 4880 helix: 2.18 (0.14), residues: 1160 sheet: 0.98 (0.11), residues: 1840 loop : -1.11 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP W 150 PHE 0.011 0.001 PHE 3 76 TYR 0.008 0.001 TYR X 86 ARG 0.003 0.000 ARG a 43 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1720) hydrogen bonds : angle 5.51058 ( 4680) covalent geometry : bond 0.00407 (34840) covalent geometry : angle 0.54781 (47840) *********************** 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 191 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 124 time to evaluate : 3.450 Fit side-chains REVERT: J 66 GLU cc_start: 0.8752 (tt0) cc_final: 0.8543 (tt0) REVERT: S 124 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: X 124 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8928 (tt0) REVERT: b 124 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.9044 (tt0) outliers start: 67 outliers final: 59 residues processed: 184 average time/residue: 1.2669 time to fit residues: 287.8614 Evaluate side-chains 182 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 3.376 ------------------------------------------------------------------------------- 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 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 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 101 THR Chi-restraints excluded: chain O residue 103 VAL 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 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 77 SER 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 b residue 124 GLU Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 83 GLN Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 119 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 307 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.2732 r_free = 0.2732 target = 0.048315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.045604 restraints weight = 112584.523| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.30 r_work: 0.2587 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 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 : 0.008 0.048 34840 Z= 0.306 Angle : 0.709 9.762 47840 Z= 0.392 Chirality : 0.056 0.168 6360 Planarity : 0.006 0.052 6080 Dihedral : 6.402 57.562 5192 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.64 % Allowed : 13.08 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 4880 helix: 1.61 (0.14), residues: 1160 sheet: 0.88 (0.11), residues: 1840 loop : -1.05 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP W 150 PHE 0.020 0.003 PHE R 76 TYR 0.014 0.002 TYR X 86 ARG 0.006 0.001 ARG 9 148 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 1720) hydrogen bonds : angle 5.90946 ( 4680) covalent geometry : bond 0.00768 (34840) covalent geometry : angle 0.70913 (47840) *********************** 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 211 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 115 time to evaluate : 3.737 Fit side-chains REVERT: J 66 GLU cc_start: 0.8795 (tt0) cc_final: 0.8587 (tt0) REVERT: N 124 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: R 100 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8941 (tp) REVERT: S 124 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: T 100 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9100 (tp) REVERT: X 124 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: 0 148 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8838 (ttm110) REVERT: 2 100 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8857 (tp) outliers start: 96 outliers final: 75 residues processed: 201 average time/residue: 1.2891 time to fit residues: 324.3187 Evaluate side-chains 198 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 116 time to evaluate : 3.499 ------------------------------------------------------------------------------- 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 E residue 154 THR 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 G residue 154 THR 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 48 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 48 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 68 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 154 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain T residue 89 THR 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 72 SER Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain U residue 144 SER 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 68 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 77 SER 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 0 residue 148 ARG 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 4 residue 103 VAL Chi-restraints excluded: chain 4 residue 114 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 6 residue 154 THR 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 48 VAL Chi-restraints excluded: chain b residue 103 VAL Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain d residue 83 GLN Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 469 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 387 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 473 optimal weight: 9.9990 chunk 454 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 228 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.047026 restraints weight = 111959.908| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.31 r_work: 0.2631 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34840 Z= 0.143 Angle : 0.523 7.392 47840 Z= 0.285 Chirality : 0.048 0.149 6360 Planarity : 0.004 0.041 6080 Dihedral : 5.770 59.848 5192 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.84 % Allowed : 13.76 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 4880 helix: 2.21 (0.14), residues: 1160 sheet: 0.93 (0.11), residues: 1840 loop : -0.98 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 150 PHE 0.009 0.001 PHE 3 76 TYR 0.007 0.001 TYR X 86 ARG 0.003 0.000 ARG U 43 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 1720) hydrogen bonds : angle 5.41673 ( 4680) covalent geometry : bond 0.00344 (34840) covalent geometry : angle 0.52317 (47840) *********************** 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 193 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 3.598 Fit side-chains REVERT: S 124 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: X 124 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8889 (tt0) outliers start: 67 outliers final: 59 residues processed: 186 average time/residue: 1.3822 time to fit residues: 317.3323 Evaluate side-chains 184 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 3.792 ------------------------------------------------------------------------------- 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 48 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 G residue 154 THR 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 68 VAL Chi-restraints excluded: chain N residue 103 VAL 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 48 VAL Chi-restraints excluded: chain Q residue 68 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 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 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 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 5 residue 144 SER Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 154 THR 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 316 optimal weight: 9.9990 chunk 417 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 403 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.2739 r_free = 0.2739 target = 0.048566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.045848 restraints weight = 112302.373| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 1.31 r_work: 0.2595 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 34840 Z= 0.267 Angle : 0.664 9.088 47840 Z= 0.366 Chirality : 0.054 0.163 6360 Planarity : 0.006 0.048 6080 Dihedral : 6.275 58.030 5192 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.31 % Allowed : 13.27 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.11), residues: 4880 helix: 1.81 (0.14), residues: 1160 sheet: 0.87 (0.11), residues: 1840 loop : -1.02 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP W 150 PHE 0.018 0.002 PHE R 76 TYR 0.012 0.002 TYR X 86 ARG 0.006 0.001 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 1720) hydrogen bonds : angle 5.80949 ( 4680) covalent geometry : bond 0.00669 (34840) covalent geometry : angle 0.66373 (47840) *********************** 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 200 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 116 time to evaluate : 3.885 Fit side-chains REVERT: N 124 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: S 124 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: X 124 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8933 (tt0) REVERT: 0 148 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8887 (ttm110) REVERT: 2 100 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8856 (tp) outliers start: 84 outliers final: 73 residues processed: 190 average time/residue: 1.2603 time to fit residues: 297.8673 Evaluate side-chains 194 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 116 time to evaluate : 3.565 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 89 THR 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 G residue 154 THR 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 72 SER 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 48 VAL Chi-restraints excluded: chain Q residue 68 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 89 THR 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 48 VAL 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 101 THR 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 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 148 ARG 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 48 VAL 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 72 SER 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 6 residue 154 THR 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 c residue 108 GLU Chi-restraints excluded: chain d residue 83 GLN 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 366 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 = 0.2761 r_free = 0.2761 target = 0.049293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.046563 restraints weight = 111908.992| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 1.31 r_work: 0.2618 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34840 Z= 0.181 Angle : 0.562 7.314 47840 Z= 0.307 Chirality : 0.049 0.152 6360 Planarity : 0.004 0.042 6080 Dihedral : 5.956 59.550 5192 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.31 % Allowed : 13.43 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 4880 helix: 2.06 (0.14), residues: 1160 sheet: 0.90 (0.11), residues: 1840 loop : -0.98 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 150 PHE 0.012 0.001 PHE 3 76 TYR 0.009 0.001 TYR X 86 ARG 0.003 0.000 ARG U 43 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 1720) hydrogen bonds : angle 5.54889 ( 4680) covalent geometry : bond 0.00443 (34840) covalent geometry : angle 0.56180 (47840) *********************** 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 203 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 119 time to evaluate : 3.793 Fit side-chains REVERT: S 124 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: X 124 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8894 (tt0) REVERT: 0 148 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8954 (ttm110) REVERT: 2 100 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8789 (tp) outliers start: 84 outliers final: 75 residues processed: 196 average time/residue: 1.2357 time to fit residues: 302.7197 Evaluate side-chains 198 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 119 time to evaluate : 3.443 ------------------------------------------------------------------------------- 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 48 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 89 THR 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 G residue 154 THR 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 48 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 103 VAL 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 48 VAL Chi-restraints excluded: chain Q residue 68 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 89 THR 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 48 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain U residue 144 SER 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 101 THR 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 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 148 ARG 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 48 VAL Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 68 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 4 residue 114 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 6 residue 154 THR 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 83 GLN 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 194 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 chunk 396 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.048337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.045623 restraints weight = 112774.295| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.31 r_work: 0.2588 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 34840 Z= 0.306 Angle : 0.706 9.760 47840 Z= 0.391 Chirality : 0.056 0.168 6360 Planarity : 0.006 0.052 6080 Dihedral : 6.403 59.204 5192 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.45 % Allowed : 13.38 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 4880 helix: 1.55 (0.14), residues: 1160 sheet: 0.85 (0.11), residues: 1840 loop : -1.05 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP W 150 PHE 0.020 0.003 PHE R 76 TYR 0.014 0.002 TYR X 86 ARG 0.007 0.001 ARG 9 148 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 1720) hydrogen bonds : angle 5.88736 ( 4680) covalent geometry : bond 0.00769 (34840) covalent geometry : angle 0.70646 (47840) ********************** 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 204 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 115 time to evaluate : 3.474 Fit side-chains REVERT: N 124 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8657 (tt0) REVERT: S 124 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: X 124 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: 0 148 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8869 (ttm110) REVERT: 2 100 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8849 (tp) outliers start: 89 outliers final: 81 residues processed: 197 average time/residue: 1.1672 time to fit residues: 288.9706 Evaluate side-chains 201 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 115 time to evaluate : 3.631 ------------------------------------------------------------------------------- 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 48 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 89 THR 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 G residue 154 THR 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 48 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 48 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 48 VAL Chi-restraints excluded: chain Q residue 68 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 89 THR 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 48 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain U residue 144 SER 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 101 THR 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 48 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 148 ARG 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 48 VAL Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 3 residue 68 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 4 residue 72 SER Chi-restraints excluded: chain 4 residue 103 VAL Chi-restraints excluded: chain 4 residue 114 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 6 residue 154 THR 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 c residue 103 VAL Chi-restraints excluded: chain d residue 83 GLN 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 242 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 360 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 186 optimal weight: 0.5980 chunk 222 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.2785 r_free = 0.2785 target = 0.050100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.047372 restraints weight = 111603.817| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 1.31 r_work: 0.2642 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2338 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= 0.122 Angle : 0.501 7.446 47840 Z= 0.271 Chirality : 0.047 0.146 6360 Planarity : 0.004 0.042 6080 Dihedral : 5.647 59.141 5192 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.92 % Allowed : 13.96 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 4880 helix: 2.30 (0.14), residues: 1160 sheet: 0.92 (0.11), residues: 1840 loop : -0.97 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 150 PHE 0.008 0.001 PHE U 76 TYR 0.006 0.001 TYR X 86 ARG 0.003 0.000 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1720) hydrogen bonds : angle 5.31656 ( 4680) covalent geometry : bond 0.00287 (34840) covalent geometry : angle 0.50065 (47840) =============================================================================== Job complete usr+sys time: 17419.39 seconds wall clock time: 298 minutes 17.85 seconds (17897.85 seconds total)