Starting phenix.real_space_refine on Thu Sep 26 21:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/09_2024/6sd5_10149.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/09_2024/6sd5_10149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/09_2024/6sd5_10149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/09_2024/6sd5_10149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/09_2024/6sd5_10149.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/09_2024/6sd5_10149.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 8844 2.51 5 N 2530 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14212 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Restraints were copied for chains: C, D, G, F, I, J, M, L, O, P, R, U, T, W, X, Z, a, c, d, g, f Time building chain proxies: 4.57, per 1000 atoms: 0.32 Number of scatterers: 14212 At special positions: 0 Unit cell: (171.798, 170.154, 41.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2816 8.00 N 2530 7.00 C 8844 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: 3.38 Conformation dependent library (CDL) restraints added in 2.0 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 44 sheets defined 38.6% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR F 146 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 200 removed outlier: 4.400A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR I 146 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 198 " --> pdb=" O VAL I 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL J 194 " --> pdb=" O GLN J 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL L 198 " --> pdb=" O VAL L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR M 146 " --> pdb=" O ARG M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 194 " --> pdb=" O GLN M 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL M 198 " --> pdb=" O VAL M 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL O 194 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL O 198 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR P 146 " --> pdb=" O ARG P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL P 194 " --> pdb=" O GLN P 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL P 198 " --> pdb=" O VAL P 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR T 146 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL T 198 " --> pdb=" O VAL T 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR U 146 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA U 193 " --> pdb=" O GLY U 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL U 198 " --> pdb=" O VAL U 194 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL W 198 " --> pdb=" O VAL W 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 132 Processing helix chain 'X' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR X 146 " --> pdb=" O ARG X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA X 193 " --> pdb=" O GLY X 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL X 194 " --> pdb=" O GLN X 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL X 198 " --> pdb=" O VAL X 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'Z' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR Z 146 " --> pdb=" O ARG Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA Z 193 " --> pdb=" O GLY Z 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL Z 198 " --> pdb=" O VAL Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 132 Processing helix chain 'a' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR a 146 " --> pdb=" O ARG a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA a 193 " --> pdb=" O GLY a 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 194 " --> pdb=" O GLN a 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 132 Processing helix chain 'c' and resid 132 through 146 removed outlier: 3.632A pdb=" N THR c 146 " --> pdb=" O ARG c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA c 193 " --> pdb=" O GLY c 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL c 198 " --> pdb=" O VAL c 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 132 Processing helix chain 'd' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA d 193 " --> pdb=" O GLY d 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL d 194 " --> pdb=" O GLN d 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL d 198 " --> pdb=" O VAL d 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 132 Processing helix chain 'f' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR f 146 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA f 193 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL f 194 " --> pdb=" O GLN f 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL f 198 " --> pdb=" O VAL f 194 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 132 Processing helix chain 'g' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER g 192 " --> pdb=" O GLU g 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA g 193 " --> pdb=" O GLY g 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL g 194 " --> pdb=" O GLN g 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL g 198 " --> pdb=" O VAL g 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR A 179 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS A 156 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR C 179 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS C 156 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR D 179 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS D 156 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR F 179 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS F 156 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR G 179 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS G 156 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR I 179 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS I 156 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR J 179 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS J 156 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR L 179 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 156 through 157 removed outlier: 3.546A pdb=" N HIS L 156 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR M 179 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS M 156 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR O 179 " --> pdb=" O LYS O 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS O 156 " --> pdb=" O SER O 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR P 179 " --> pdb=" O LYS P 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS P 156 " --> pdb=" O SER P 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR R 179 " --> pdb=" O LYS R 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS R 156 " --> pdb=" O SER R 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR T 179 " --> pdb=" O LYS T 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS T 156 " --> pdb=" O SER T 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR U 179 " --> pdb=" O LYS U 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS U 156 " --> pdb=" O SER U 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR W 179 " --> pdb=" O LYS W 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS W 156 " --> pdb=" O SER W 175 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR X 179 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS X 156 " --> pdb=" O SER X 175 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR Z 179 " --> pdb=" O LYS Z 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS Z 156 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'a' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR a 179 " --> pdb=" O LYS a 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS a 156 " --> pdb=" O SER a 175 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR c 179 " --> pdb=" O LYS c 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS c 156 " --> pdb=" O SER c 175 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR d 179 " --> pdb=" O LYS d 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS d 156 " --> pdb=" O SER d 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR f 179 " --> pdb=" O LYS f 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'f' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS f 156 " --> pdb=" O SER f 175 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR g 179 " --> pdb=" O LYS g 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS g 156 " --> pdb=" O SER g 175 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4928 1.34 - 1.46: 1742 1.46 - 1.57: 7696 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 14410 Sorted by residual: bond pdb=" CA HIS T 218 " pdb=" C HIS T 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.06e+00 bond pdb=" CA HIS O 218 " pdb=" C HIS O 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.88e+00 bond pdb=" CA HIS g 218 " pdb=" C HIS g 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.86e+00 bond pdb=" CA HIS G 218 " pdb=" C HIS G 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.86e+00 bond pdb=" CA HIS A 218 " pdb=" C HIS A 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.83e+00 ... (remaining 14405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 17298 0.94 - 1.88: 1856 1.88 - 2.83: 316 2.83 - 3.77: 117 3.77 - 4.71: 59 Bond angle restraints: 19646 Sorted by residual: angle pdb=" N VAL J 130 " pdb=" CA VAL J 130 " pdb=" C VAL J 130 " ideal model delta sigma weight residual 112.12 108.28 3.84 8.40e-01 1.42e+00 2.08e+01 angle pdb=" N VAL L 130 " pdb=" CA VAL L 130 " pdb=" C VAL L 130 " ideal model delta sigma weight residual 112.12 108.30 3.82 8.40e-01 1.42e+00 2.07e+01 angle pdb=" N VAL O 130 " pdb=" CA VAL O 130 " pdb=" C VAL O 130 " ideal model delta sigma weight residual 112.12 108.30 3.82 8.40e-01 1.42e+00 2.06e+01 angle pdb=" N VAL a 130 " pdb=" CA VAL a 130 " pdb=" C VAL a 130 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 angle pdb=" N VAL M 130 " pdb=" CA VAL M 130 " pdb=" C VAL M 130 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 ... (remaining 19641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 7832 16.44 - 32.88: 726 32.88 - 49.32: 176 49.32 - 65.76: 44 65.76 - 82.20: 22 Dihedral angle restraints: 8800 sinusoidal: 3322 harmonic: 5478 Sorted by residual: dihedral pdb=" CB GLU J 188 " pdb=" CG GLU J 188 " pdb=" CD GLU J 188 " pdb=" OE1 GLU J 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.20 82.20 1 3.00e+01 1.11e-03 9.22e+00 dihedral pdb=" CB GLU R 188 " pdb=" CG GLU R 188 " pdb=" CD GLU R 188 " pdb=" OE1 GLU R 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.16 82.16 1 3.00e+01 1.11e-03 9.21e+00 dihedral pdb=" CB GLU D 188 " pdb=" CG GLU D 188 " pdb=" CD GLU D 188 " pdb=" OE1 GLU D 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.16 82.16 1 3.00e+01 1.11e-03 9.21e+00 ... (remaining 8797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1365 0.028 - 0.055: 656 0.055 - 0.083: 284 0.083 - 0.110: 115 0.110 - 0.138: 22 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CA VAL f 213 " pdb=" N VAL f 213 " pdb=" C VAL f 213 " pdb=" CB VAL f 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL W 213 " pdb=" N VAL W 213 " pdb=" C VAL W 213 " pdb=" CB VAL W 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2439 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU T 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO T 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO T 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO T 182 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU a 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.59e-01 pdb=" N PRO a 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO a 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO a 182 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU d 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.59e-01 pdb=" N PRO d 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO d 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO d 182 " -0.010 5.00e-02 4.00e+02 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5059 2.84 - 3.35: 13320 3.35 - 3.87: 21809 3.87 - 4.38: 27851 4.38 - 4.90: 47853 Nonbonded interactions: 115892 Sorted by model distance: nonbonded pdb=" O SER D 175 " pdb=" OG SER D 175 " model vdw 2.321 3.040 nonbonded pdb=" O SER L 175 " pdb=" OG SER L 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER F 175 " pdb=" OG SER F 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER A 175 " pdb=" OG SER A 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER I 175 " pdb=" OG SER I 175 " model vdw 2.322 3.040 ... (remaining 115887 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' } 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: 3.300 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 29.760 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 0.041 14410 Z= 0.431 Angle : 0.708 4.709 19646 Z= 0.428 Chirality : 0.041 0.138 2442 Planarity : 0.003 0.019 2574 Dihedral : 15.042 82.197 5236 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % 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: -5.48 (0.16), residues: 1848 helix: -4.59 (0.08), residues: 726 sheet: -3.31 (0.23), residues: 484 loop : -2.12 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS f 156 PHE 0.007 0.002 PHE g 126 TYR 0.004 0.001 TYR R 132 ARG 0.002 0.000 ARG I 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 447 time to evaluate : 1.641 Fit side-chains REVERT: A 129 GLN cc_start: 0.7441 (mp10) cc_final: 0.7201 (mp10) REVERT: A 218 HIS cc_start: 0.7081 (m-70) cc_final: 0.6794 (t-90) REVERT: C 218 HIS cc_start: 0.7060 (m-70) cc_final: 0.6816 (t-90) REVERT: D 129 GLN cc_start: 0.7408 (mp10) cc_final: 0.7205 (mp10) REVERT: F 129 GLN cc_start: 0.7415 (mp10) cc_final: 0.7132 (mp10) REVERT: F 218 HIS cc_start: 0.6911 (m-70) cc_final: 0.6616 (t-90) REVERT: G 129 GLN cc_start: 0.7552 (mp10) cc_final: 0.7352 (mp10) REVERT: G 134 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7405 (mtm110) REVERT: I 134 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7433 (mtm110) REVERT: I 218 HIS cc_start: 0.6939 (m-70) cc_final: 0.6688 (t-90) REVERT: J 129 GLN cc_start: 0.7478 (mp10) cc_final: 0.7201 (mp10) REVERT: J 218 HIS cc_start: 0.7011 (m-70) cc_final: 0.6726 (t-90) REVERT: L 134 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7407 (mtm110) REVERT: L 197 LEU cc_start: 0.8692 (tp) cc_final: 0.8357 (tt) REVERT: M 134 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7269 (mtm110) REVERT: O 134 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7254 (mtm110) REVERT: P 134 ARG cc_start: 0.7467 (mtp180) cc_final: 0.7225 (mtm110) REVERT: R 129 GLN cc_start: 0.7404 (mp10) cc_final: 0.7162 (mp10) REVERT: T 134 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7186 (mtm110) REVERT: U 129 GLN cc_start: 0.7535 (mp10) cc_final: 0.7334 (mp10) REVERT: U 134 ARG cc_start: 0.7495 (mtp180) cc_final: 0.7291 (mtm110) REVERT: U 142 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7384 (mmt-90) REVERT: W 129 GLN cc_start: 0.7484 (mp10) cc_final: 0.7248 (mp10) REVERT: W 134 ARG cc_start: 0.7620 (mtp180) cc_final: 0.7405 (mtm110) REVERT: X 134 ARG cc_start: 0.7667 (mtp180) cc_final: 0.7432 (mtm110) REVERT: Z 218 HIS cc_start: 0.7001 (m-70) cc_final: 0.6740 (t-90) REVERT: a 129 GLN cc_start: 0.7473 (mp10) cc_final: 0.7211 (mp10) REVERT: a 218 HIS cc_start: 0.6905 (m-70) cc_final: 0.6669 (t-90) REVERT: c 197 LEU cc_start: 0.8725 (tp) cc_final: 0.8500 (tt) REVERT: c 218 HIS cc_start: 0.6958 (m-70) cc_final: 0.6739 (t-90) REVERT: g 127 SER cc_start: 0.8706 (t) cc_final: 0.8484 (t) REVERT: g 218 HIS cc_start: 0.7003 (m-70) cc_final: 0.6643 (t-90) outliers start: 22 outliers final: 20 residues processed: 469 average time/residue: 0.2908 time to fit residues: 188.5507 Evaluate side-chains 414 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 394 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain Z residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain g residue 214 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 83 optimal weight: 0.0000 chunk 102 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 196 HIS C 196 HIS D 196 HIS F 190 GLN F 196 HIS G 190 GLN G 196 HIS I 190 GLN J 196 HIS L 190 GLN M 190 GLN M 196 HIS O 190 GLN O 196 HIS P 190 GLN P 196 HIS R 190 GLN R 196 HIS T 196 HIS U 196 HIS W 190 GLN X 196 HIS Z 190 GLN Z 196 HIS a 196 HIS c 196 HIS d 190 GLN d 196 HIS f 190 GLN f 196 HIS g 196 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14410 Z= 0.193 Angle : 0.558 6.606 19646 Z= 0.286 Chirality : 0.038 0.116 2442 Planarity : 0.004 0.017 2574 Dihedral : 4.061 11.487 2042 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.28 % Allowed : 16.35 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.17), residues: 1848 helix: -2.90 (0.15), residues: 770 sheet: -2.89 (0.23), residues: 484 loop : -1.62 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS U 156 PHE 0.005 0.001 PHE d 126 TYR 0.002 0.001 TYR I 132 ARG 0.008 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 449 time to evaluate : 1.626 Fit side-chains REVERT: A 129 GLN cc_start: 0.7437 (mp10) cc_final: 0.7181 (mp10) REVERT: D 129 GLN cc_start: 0.7347 (mp10) cc_final: 0.7094 (mp10) REVERT: F 129 GLN cc_start: 0.7374 (mp10) cc_final: 0.7171 (mp10) REVERT: G 129 GLN cc_start: 0.7584 (mp10) cc_final: 0.7294 (mp10) REVERT: J 129 GLN cc_start: 0.7395 (mp10) cc_final: 0.7133 (mp10) REVERT: R 129 GLN cc_start: 0.7409 (mp10) cc_final: 0.7124 (mp10) REVERT: U 129 GLN cc_start: 0.7409 (mp10) cc_final: 0.7132 (mp10) REVERT: a 129 GLN cc_start: 0.7371 (mp10) cc_final: 0.7044 (mp10) REVERT: c 142 ARG cc_start: 0.7853 (tpp-160) cc_final: 0.7393 (ttm-80) REVERT: d 142 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7361 (ttm-80) REVERT: f 142 ARG cc_start: 0.7964 (tpp-160) cc_final: 0.7640 (ttm-80) REVERT: g 142 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7611 (ttm-80) REVERT: g 218 HIS cc_start: 0.6870 (m-70) cc_final: 0.6597 (t-90) outliers start: 52 outliers final: 33 residues processed: 480 average time/residue: 0.2572 time to fit residues: 177.1496 Evaluate side-chains 413 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 380 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 142 optimal weight: 0.0570 chunk 158 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 209 ASN G 190 GLN I 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN U 209 ASN c 190 GLN f 190 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14410 Z= 0.163 Angle : 0.534 8.477 19646 Z= 0.265 Chirality : 0.040 0.137 2442 Planarity : 0.003 0.027 2574 Dihedral : 3.554 10.832 2002 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.41 % Allowed : 19.38 % Favored : 77.21 % 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: -2.95 (0.19), residues: 1848 helix: -1.37 (0.18), residues: 770 sheet: -2.83 (0.22), residues: 528 loop : -1.32 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 156 PHE 0.006 0.001 PHE T 126 TYR 0.001 0.000 TYR O 132 ARG 0.007 0.001 ARG Z 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 404 time to evaluate : 1.631 Fit side-chains REVERT: A 129 GLN cc_start: 0.7398 (mp10) cc_final: 0.7121 (mp10) REVERT: C 142 ARG cc_start: 0.7853 (tpp-160) cc_final: 0.7331 (ttm-80) REVERT: D 129 GLN cc_start: 0.7298 (mp10) cc_final: 0.7065 (mp10) REVERT: F 129 GLN cc_start: 0.7390 (mp10) cc_final: 0.7179 (mp10) REVERT: G 129 GLN cc_start: 0.7491 (mp10) cc_final: 0.7217 (mp10) REVERT: R 129 GLN cc_start: 0.7336 (mp10) cc_final: 0.7071 (mp10) REVERT: U 129 GLN cc_start: 0.7368 (mp10) cc_final: 0.7102 (mp10) REVERT: c 142 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7353 (ttm-80) REVERT: d 142 ARG cc_start: 0.7845 (tpp-160) cc_final: 0.7367 (ttm-80) REVERT: f 142 ARG cc_start: 0.7914 (tpp-160) cc_final: 0.7630 (ttm-80) REVERT: g 142 ARG cc_start: 0.7879 (tpp-160) cc_final: 0.7391 (ttm-80) outliers start: 54 outliers final: 37 residues processed: 438 average time/residue: 0.2658 time to fit residues: 165.6609 Evaluate side-chains 420 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 383 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 192 SER Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 0.0020 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN G 190 GLN I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN W 190 GLN c 190 GLN f 190 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14410 Z= 0.209 Angle : 0.547 7.882 19646 Z= 0.268 Chirality : 0.040 0.124 2442 Planarity : 0.003 0.029 2574 Dihedral : 3.488 12.478 2002 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.36 % Allowed : 18.50 % Favored : 77.15 % 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: -2.21 (0.20), residues: 1848 helix: -0.84 (0.19), residues: 770 sheet: -2.47 (0.25), residues: 484 loop : -0.97 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 156 PHE 0.006 0.001 PHE W 126 TYR 0.002 0.000 TYR O 132 ARG 0.006 0.001 ARG Z 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 384 time to evaluate : 1.580 Fit side-chains REVERT: A 129 GLN cc_start: 0.7337 (mp10) cc_final: 0.7105 (mp10) REVERT: D 129 GLN cc_start: 0.7295 (mp10) cc_final: 0.7077 (mp10) REVERT: F 129 GLN cc_start: 0.7404 (mp10) cc_final: 0.7188 (mp10) REVERT: c 142 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7275 (ttm-80) REVERT: d 142 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7341 (ttm-80) REVERT: f 142 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7561 (ttm-80) outliers start: 69 outliers final: 59 residues processed: 428 average time/residue: 0.2576 time to fit residues: 157.7787 Evaluate side-chains 420 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 361 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 152 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN W 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14410 Z= 0.244 Angle : 0.568 8.957 19646 Z= 0.274 Chirality : 0.041 0.121 2442 Planarity : 0.003 0.032 2574 Dihedral : 3.509 14.099 2002 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.74 % Allowed : 17.68 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1848 helix: -0.70 (0.19), residues: 770 sheet: -2.35 (0.25), residues: 484 loop : -0.84 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 156 PHE 0.006 0.001 PHE T 126 TYR 0.002 0.000 TYR P 132 ARG 0.008 0.001 ARG Z 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 361 time to evaluate : 2.100 Fit side-chains REVERT: A 129 GLN cc_start: 0.7339 (mp10) cc_final: 0.7138 (mp10) REVERT: L 190 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: d 142 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7370 (ttm-80) outliers start: 91 outliers final: 77 residues processed: 419 average time/residue: 0.2514 time to fit residues: 152.8892 Evaluate side-chains 425 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 347 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 152 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 152 SER Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 190 GLN Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 0.0030 chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN L 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN W 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14410 Z= 0.215 Angle : 0.551 7.920 19646 Z= 0.268 Chirality : 0.040 0.120 2442 Planarity : 0.003 0.034 2574 Dihedral : 3.424 14.874 2002 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.06 % Allowed : 18.31 % Favored : 75.63 % 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: -1.81 (0.20), residues: 1848 helix: -0.57 (0.20), residues: 770 sheet: -2.24 (0.25), residues: 484 loop : -0.69 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 156 PHE 0.006 0.001 PHE F 126 TYR 0.001 0.000 TYR O 132 ARG 0.008 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 364 time to evaluate : 1.648 Fit side-chains REVERT: L 190 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: d 142 ARG cc_start: 0.7986 (tpp-160) cc_final: 0.7363 (ttm-80) outliers start: 96 outliers final: 85 residues processed: 423 average time/residue: 0.2432 time to fit residues: 149.9416 Evaluate side-chains 437 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 351 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 159 MET Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 152 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 152 SER Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 190 GLN Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN W 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14410 Z= 0.250 Angle : 0.562 7.528 19646 Z= 0.273 Chirality : 0.041 0.122 2442 Planarity : 0.003 0.035 2574 Dihedral : 3.449 15.939 2002 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.01 % Allowed : 17.55 % Favored : 75.44 % 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: -1.74 (0.20), residues: 1848 helix: -0.59 (0.20), residues: 770 sheet: -2.09 (0.25), residues: 484 loop : -0.65 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 156 PHE 0.006 0.001 PHE F 126 TYR 0.002 0.001 TYR W 132 ARG 0.009 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 351 time to evaluate : 1.777 Fit side-chains REVERT: L 190 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7618 (tt0) outliers start: 111 outliers final: 101 residues processed: 420 average time/residue: 0.2489 time to fit residues: 152.4047 Evaluate side-chains 446 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 344 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 159 MET Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 152 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain f residue 221 THR Chi-restraints excluded: chain g residue 152 SER Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 190 GLN Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 0.0030 chunk 15 optimal weight: 0.5980 chunk 133 optimal weight: 0.2980 chunk 154 optimal weight: 0.7980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN L 190 GLN M 190 GLN O 190 GLN O 209 ASN P 190 GLN R 190 GLN U 190 GLN W 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14410 Z= 0.183 Angle : 0.535 6.820 19646 Z= 0.262 Chirality : 0.040 0.129 2442 Planarity : 0.003 0.033 2574 Dihedral : 3.272 15.412 2002 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.49 % Allowed : 19.32 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.20), residues: 1848 helix: -0.42 (0.20), residues: 770 sheet: -2.00 (0.25), residues: 484 loop : -0.46 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 156 PHE 0.005 0.001 PHE c 126 TYR 0.002 0.000 TYR O 132 ARG 0.008 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 377 time to evaluate : 1.489 Fit side-chains REVERT: L 190 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: c 197 LEU cc_start: 0.8509 (tt) cc_final: 0.8230 (tt) outliers start: 87 outliers final: 76 residues processed: 434 average time/residue: 0.2362 time to fit residues: 150.8565 Evaluate side-chains 437 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 360 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 159 MET Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 190 GLN Chi-restraints excluded: chain g residue 197 LEU Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.3980 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN L 190 GLN M 190 GLN O 190 GLN O 209 ASN P 190 GLN R 190 GLN U 190 GLN W 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14410 Z= 0.236 Angle : 0.564 8.604 19646 Z= 0.273 Chirality : 0.041 0.120 2442 Planarity : 0.004 0.044 2574 Dihedral : 3.344 16.273 2002 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.74 % Allowed : 19.76 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1848 helix: -0.44 (0.20), residues: 770 sheet: -1.87 (0.25), residues: 484 loop : -0.46 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 156 PHE 0.006 0.001 PHE L 126 TYR 0.002 0.000 TYR O 132 ARG 0.012 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 349 time to evaluate : 1.588 Fit side-chains REVERT: L 190 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7574 (tt0) outliers start: 91 outliers final: 83 residues processed: 410 average time/residue: 0.2496 time to fit residues: 149.2569 Evaluate side-chains 429 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 345 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 159 MET Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain f residue 221 THR Chi-restraints excluded: chain g residue 152 SER Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 190 GLN Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.0870 chunk 102 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN W 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14410 Z= 0.222 Angle : 0.566 8.252 19646 Z= 0.276 Chirality : 0.041 0.127 2442 Planarity : 0.004 0.041 2574 Dihedral : 3.317 16.273 2002 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.81 % Allowed : 20.14 % Favored : 74.05 % 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: -1.41 (0.20), residues: 1848 helix: -0.41 (0.19), residues: 770 sheet: -1.80 (0.25), residues: 484 loop : -0.43 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 156 PHE 0.005 0.001 PHE d 126 TYR 0.002 0.000 TYR O 132 ARG 0.010 0.001 ARG G 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 357 time to evaluate : 1.461 Fit side-chains outliers start: 92 outliers final: 83 residues processed: 415 average time/residue: 0.2481 time to fit residues: 150.4379 Evaluate side-chains 433 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 350 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 159 MET Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain f residue 221 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 197 LEU Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.0470 chunk 122 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN F 190 GLN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN O 190 GLN O 209 ASN P 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124989 restraints weight = 16093.705| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.05 r_work: 0.3344 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14410 Z= 0.218 Angle : 0.561 8.112 19646 Z= 0.273 Chirality : 0.041 0.128 2442 Planarity : 0.004 0.039 2574 Dihedral : 3.298 16.587 2002 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.00 % Allowed : 20.01 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1848 helix: -0.39 (0.19), residues: 770 sheet: -1.73 (0.25), residues: 484 loop : -0.42 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 156 PHE 0.005 0.001 PHE L 126 TYR 0.001 0.000 TYR g 132 ARG 0.010 0.001 ARG M 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3934.53 seconds wall clock time: 71 minutes 9.52 seconds (4269.52 seconds total)