Starting phenix.real_space_refine on Fri Mar 14 06:20:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cda_45465/03_2025/9cda_45465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cda_45465/03_2025/9cda_45465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cda_45465/03_2025/9cda_45465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cda_45465/03_2025/9cda_45465.map" model { file = "/net/cci-nas-00/data/ceres_data/9cda_45465/03_2025/9cda_45465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cda_45465/03_2025/9cda_45465.cif" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6111 2.51 5 N 1737 2.21 5 O 2007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 2 Chain: "a" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 538 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "b" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 557 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Restraints were copied for chains: K, M, O, Q, S, U, W, Y, L, N, P, R, T, V, X, Z Time building chain proxies: 2.81, per 1000 atoms: 0.29 Number of scatterers: 9855 At special positions: 0 Unit cell: (110.922, 97.578, 63.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2007 8.00 N 1737 7.00 C 6111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'M' and resid 15 through 20 removed outlier: 6.375A pdb=" N VAL K 15 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA S 18 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA K 17 " --> pdb=" O ALA S 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU S 20 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA K 19 " --> pdb=" O GLU S 20 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL Q 15 " --> pdb=" O VAL W 16 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA W 18 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA Q 17 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU W 20 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA Q 19 " --> pdb=" O GLU W 20 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL U 15 " --> pdb=" O VAL a 16 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA a 18 " --> pdb=" O VAL U 15 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA U 17 " --> pdb=" O ALA a 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU a 20 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA U 19 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL Y 15 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA O 18 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA Y 17 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU O 20 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA Y 19 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 24 through 34 removed outlier: 6.217A pdb=" N GLN K 24 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA M 27 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL K 26 " --> pdb=" O ALA M 27 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA M 29 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU K 28 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLY M 31 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ALA K 30 " --> pdb=" O GLY M 31 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR M 33 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS K 32 " --> pdb=" O THR M 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS S 32 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR K 33 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS S 34 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN Q 24 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA S 27 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Q 26 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA S 29 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU Q 28 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY S 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ALA Q 30 " --> pdb=" O GLY S 31 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR S 33 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS Q 32 " --> pdb=" O THR S 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS W 32 " --> pdb=" O GLY Q 31 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR Q 33 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS W 34 " --> pdb=" O THR Q 33 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN U 24 " --> pdb=" O GLY W 25 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA W 27 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL U 26 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA W 29 " --> pdb=" O VAL U 26 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU U 28 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLY W 31 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ALA U 30 " --> pdb=" O GLY W 31 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR W 33 " --> pdb=" O ALA U 30 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS U 32 " --> pdb=" O THR W 33 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS a 32 " --> pdb=" O GLY U 31 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR U 33 " --> pdb=" O LYS a 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS a 34 " --> pdb=" O THR U 33 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN Y 24 " --> pdb=" O GLY a 25 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA a 27 " --> pdb=" O GLN Y 24 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Y 26 " --> pdb=" O ALA a 27 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA a 29 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU Y 28 " --> pdb=" O ALA a 29 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY a 31 " --> pdb=" O GLU Y 28 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ALA Y 30 " --> pdb=" O GLY a 31 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR a 33 " --> pdb=" O ALA Y 30 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LYS Y 32 " --> pdb=" O THR a 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS O 32 " --> pdb=" O GLY Y 31 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR Y 33 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS O 34 " --> pdb=" O THR Y 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 38 through 40 removed outlier: 6.472A pdb=" N TYR K 39 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR Q 39 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR U 39 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR Y 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 46 through 55 removed outlier: 6.906A pdb=" N GLY M 47 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL K 52 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA M 53 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR K 54 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL M 55 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY K 47 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N HIS S 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL K 49 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL S 52 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY K 51 " --> pdb=" O VAL S 52 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N THR S 54 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA K 53 " --> pdb=" O THR S 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY S 47 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL Q 52 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA S 53 " --> pdb=" O VAL Q 52 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR Q 54 " --> pdb=" O ALA S 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL S 55 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY Q 47 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS W 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL Q 49 " --> pdb=" O HIS W 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL W 52 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY Q 51 " --> pdb=" O VAL W 52 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N THR W 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA Q 53 " --> pdb=" O THR W 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY W 47 " --> pdb=" O GLU U 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL U 52 " --> pdb=" O GLY W 51 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA W 53 " --> pdb=" O VAL U 52 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR U 54 " --> pdb=" O ALA W 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL W 55 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY U 47 " --> pdb=" O VAL a 48 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N HIS a 50 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL U 49 " --> pdb=" O HIS a 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL a 52 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY U 51 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N THR a 54 " --> pdb=" O GLY U 51 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ALA U 53 " --> pdb=" O THR a 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY a 47 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL Y 52 " --> pdb=" O GLY a 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA a 53 " --> pdb=" O VAL Y 52 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR Y 54 " --> pdb=" O ALA a 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL a 55 " --> pdb=" O THR Y 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY Y 47 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS O 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL Y 49 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL O 52 " --> pdb=" O VAL Y 49 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY Y 51 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N THR O 54 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA Y 53 " --> pdb=" O THR O 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 69 through 71 removed outlier: 6.498A pdb=" N ALA K 69 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA Q 69 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA U 69 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA Y 69 " --> pdb=" O VAL a 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 89 through 91 removed outlier: 6.244A pdb=" N ALA K 89 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA Q 89 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA U 89 " --> pdb=" O ALA W 90 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA Y 89 " --> pdb=" O ALA a 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 23 through 28 removed outlier: 7.022A pdb=" N GLN L 24 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY N 25 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N LYS L 23 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL T 26 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY L 25 " --> pdb=" O VAL T 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU T 28 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA L 27 " --> pdb=" O GLU T 28 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN R 24 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY T 25 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS R 23 " --> pdb=" O GLN X 24 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL X 26 " --> pdb=" O LYS R 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY R 25 " --> pdb=" O VAL X 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU X 28 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA R 27 " --> pdb=" O GLU X 28 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN V 24 " --> pdb=" O LYS X 23 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY X 25 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS V 23 " --> pdb=" O GLN b 24 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL b 26 " --> pdb=" O LYS V 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY V 25 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLU b 28 " --> pdb=" O GLY V 25 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA V 27 " --> pdb=" O GLU b 28 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN Z 24 " --> pdb=" O LYS b 23 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY b 25 " --> pdb=" O GLN Z 24 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS Z 23 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL P 26 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY Z 25 " --> pdb=" O VAL P 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU P 28 " --> pdb=" O GLY Z 25 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA Z 27 " --> pdb=" O GLU P 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 38 through 57 removed outlier: 6.866A pdb=" N TYR N 39 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL L 40 " --> pdb=" O TYR N 39 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY N 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER L 42 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS N 43 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR L 44 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS N 45 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU L 46 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY N 47 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL L 52 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA N 53 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR L 54 " --> pdb=" O ALA N 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL N 55 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA L 56 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU N 57 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N TYR L 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N SER T 42 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLY L 41 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N THR T 44 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LYS L 43 " --> pdb=" O THR T 44 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLU T 46 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS L 45 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL T 48 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY L 47 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS T 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL L 49 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL T 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY L 51 " --> pdb=" O VAL T 52 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR T 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA L 53 " --> pdb=" O THR T 54 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ALA T 56 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL L 55 " --> pdb=" O ALA T 56 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR T 39 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL R 40 " --> pdb=" O TYR T 39 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY T 41 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER R 42 " --> pdb=" O GLY T 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS T 43 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR R 44 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS T 45 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU R 46 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY T 47 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL R 52 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA T 53 " --> pdb=" O VAL R 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR R 54 " --> pdb=" O ALA T 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL T 55 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA R 56 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU T 57 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N TYR R 39 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N SER X 42 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLY R 41 " --> pdb=" O SER X 42 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N THR X 44 " --> pdb=" O GLY R 41 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N LYS R 43 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLU X 46 " --> pdb=" O LYS R 43 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS R 45 " --> pdb=" O GLU X 46 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL X 48 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY R 47 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS X 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL R 49 " --> pdb=" O HIS X 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY R 51 " --> pdb=" O VAL X 52 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N THR X 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA R 53 " --> pdb=" O THR X 54 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N ALA X 56 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL R 55 " --> pdb=" O ALA X 56 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR X 39 " --> pdb=" O LEU V 38 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL V 40 " --> pdb=" O TYR X 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY X 41 " --> pdb=" O VAL V 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER V 42 " --> pdb=" O GLY X 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS X 43 " --> pdb=" O SER V 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR V 44 " --> pdb=" O LYS X 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS X 45 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU V 46 " --> pdb=" O LYS X 45 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY X 47 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL V 52 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA X 53 " --> pdb=" O VAL V 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR V 54 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL X 55 " --> pdb=" O THR V 54 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA V 56 " --> pdb=" O VAL X 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU X 57 " --> pdb=" O ALA V 56 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N TYR V 39 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N SER b 42 " --> pdb=" O TYR V 39 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLY V 41 " --> pdb=" O SER b 42 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N THR b 44 " --> pdb=" O GLY V 41 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LYS V 43 " --> pdb=" O THR b 44 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLU b 46 " --> pdb=" O LYS V 43 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LYS V 45 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL b 48 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY V 47 " --> pdb=" O VAL b 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS b 50 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL V 49 " --> pdb=" O HIS b 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL b 52 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY V 51 " --> pdb=" O VAL b 52 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR b 54 " --> pdb=" O GLY V 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA V 53 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ALA b 56 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N VAL V 55 " --> pdb=" O ALA b 56 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR b 39 " --> pdb=" O LEU Z 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL Z 40 " --> pdb=" O TYR b 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY b 41 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER Z 42 " --> pdb=" O GLY b 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS b 43 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR Z 44 " --> pdb=" O LYS b 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS b 45 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU Z 46 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY b 47 " --> pdb=" O GLU Z 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL Z 52 " --> pdb=" O GLY b 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA b 53 " --> pdb=" O VAL Z 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR Z 54 " --> pdb=" O ALA b 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL b 55 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA Z 56 " --> pdb=" O VAL b 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU b 57 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N TYR Z 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N SER P 42 " --> pdb=" O TYR Z 39 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLY Z 41 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N THR P 44 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LYS Z 43 " --> pdb=" O THR P 44 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLU P 46 " --> pdb=" O LYS Z 43 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS Z 45 " --> pdb=" O GLU P 46 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL P 48 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY Z 47 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS P 50 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL Z 49 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL P 52 " --> pdb=" O VAL Z 49 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY Z 51 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR P 54 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA Z 53 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ALA P 56 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N VAL Z 55 " --> pdb=" O ALA P 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 60 through 66 removed outlier: 6.464A pdb=" N LYS L 60 " --> pdb=" O GLU N 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL N 63 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN L 62 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN N 65 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR L 64 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS R 60 " --> pdb=" O GLU T 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL T 63 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN R 62 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN T 65 " --> pdb=" O GLN R 62 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR R 64 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS V 60 " --> pdb=" O GLU X 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL X 63 " --> pdb=" O LYS V 60 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN V 62 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN X 65 " --> pdb=" O GLN V 62 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR V 64 " --> pdb=" O ASN X 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS Z 60 " --> pdb=" O GLU b 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL b 63 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN Z 62 " --> pdb=" O VAL b 63 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN b 65 " --> pdb=" O GLN Z 62 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR Z 64 " --> pdb=" O ASN b 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.587A pdb=" N VAL L 70 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL R 70 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL V 70 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL Z 70 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 74 through 82 removed outlier: 6.572A pdb=" N VAL L 74 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL T 77 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA L 76 " --> pdb=" O VAL T 77 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLN T 79 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA L 78 " --> pdb=" O GLN T 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR T 81 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS L 80 " --> pdb=" O THR T 81 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL R 74 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL X 77 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA R 76 " --> pdb=" O VAL X 77 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLN X 79 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA R 78 " --> pdb=" O GLN X 79 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR X 81 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS R 80 " --> pdb=" O THR X 81 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL V 74 " --> pdb=" O THR b 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL b 77 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA V 76 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLN b 79 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA V 78 " --> pdb=" O GLN b 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR b 81 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS V 80 " --> pdb=" O THR b 81 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL Z 74 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL P 77 " --> pdb=" O VAL Z 74 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA Z 76 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLN P 79 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA Z 78 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR P 81 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS Z 80 " --> pdb=" O THR P 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 88 through 96 removed outlier: 6.869A pdb=" N ALA N 89 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE L 94 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL N 95 " --> pdb=" O PHE L 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS L 96 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA L 89 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR T 92 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA L 91 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE T 94 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY L 93 " --> pdb=" O PHE T 94 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N LYS T 96 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N VAL L 95 " --> pdb=" O LYS T 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA T 89 " --> pdb=" O ILE R 88 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE R 94 " --> pdb=" O GLY T 93 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL T 95 " --> pdb=" O PHE R 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS R 96 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA R 89 " --> pdb=" O ALA X 90 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR X 92 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA R 91 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE X 94 " --> pdb=" O ALA R 91 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLY R 93 " --> pdb=" O PHE X 94 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N LYS X 96 " --> pdb=" O GLY R 93 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL R 95 " --> pdb=" O LYS X 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA X 89 " --> pdb=" O ILE V 88 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE V 94 " --> pdb=" O GLY X 93 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL X 95 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS V 96 " --> pdb=" O VAL X 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA V 89 " --> pdb=" O ALA b 90 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR b 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA V 91 " --> pdb=" O THR b 92 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE b 94 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY V 93 " --> pdb=" O PHE b 94 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N LYS b 96 " --> pdb=" O GLY V 93 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N VAL V 95 " --> pdb=" O LYS b 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA b 89 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE Z 94 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL b 95 " --> pdb=" O PHE Z 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS Z 96 " --> pdb=" O VAL b 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA Z 89 " --> pdb=" O ALA P 90 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR P 92 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA Z 91 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE P 94 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY Z 93 " --> pdb=" O PHE P 94 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N LYS P 96 " --> pdb=" O GLY Z 93 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL Z 95 " --> pdb=" O LYS P 96 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 588 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: 2.32 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1773 1.29 - 1.35: 1539 1.35 - 1.42: 269 1.42 - 1.48: 1622 1.48 - 1.54: 4679 Bond restraints: 9882 Sorted by residual: bond pdb=" C ALA O 89 " pdb=" O ALA O 89 " ideal model delta sigma weight residual 1.235 1.222 0.013 1.13e-02 7.83e+03 1.34e+00 bond pdb=" C ALA a 89 " pdb=" O ALA a 89 " ideal model delta sigma weight residual 1.235 1.223 0.013 1.13e-02 7.83e+03 1.24e+00 bond pdb=" C ALA W 89 " pdb=" O ALA W 89 " ideal model delta sigma weight residual 1.235 1.223 0.013 1.13e-02 7.83e+03 1.23e+00 bond pdb=" C ALA S 89 " pdb=" O ALA S 89 " ideal model delta sigma weight residual 1.235 1.223 0.012 1.13e-02 7.83e+03 1.15e+00 bond pdb=" C ALA M 89 " pdb=" O ALA M 89 " ideal model delta sigma weight residual 1.235 1.223 0.012 1.13e-02 7.83e+03 1.15e+00 ... (remaining 9877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 12832 1.24 - 2.49: 419 2.49 - 3.73: 51 3.73 - 4.98: 9 4.98 - 6.22: 9 Bond angle restraints: 13320 Sorted by residual: angle pdb=" C GLN S 24 " pdb=" N GLY S 25 " pdb=" CA GLY S 25 " ideal model delta sigma weight residual 122.33 120.59 1.74 7.30e-01 1.88e+00 5.67e+00 angle pdb=" C GLN W 24 " pdb=" N GLY W 25 " pdb=" CA GLY W 25 " ideal model delta sigma weight residual 122.33 120.61 1.72 7.30e-01 1.88e+00 5.56e+00 angle pdb=" C GLN M 24 " pdb=" N GLY M 25 " pdb=" CA GLY M 25 " ideal model delta sigma weight residual 122.33 120.63 1.70 7.30e-01 1.88e+00 5.45e+00 angle pdb=" C GLN Y 24 " pdb=" N GLY Y 25 " pdb=" CA GLY Y 25 " ideal model delta sigma weight residual 122.33 120.64 1.69 7.30e-01 1.88e+00 5.36e+00 angle pdb=" C GLN a 24 " pdb=" N GLY a 25 " pdb=" CA GLY a 25 " ideal model delta sigma weight residual 122.33 120.65 1.68 7.30e-01 1.88e+00 5.30e+00 ... (remaining 13315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.06: 4842 14.06 - 28.13: 594 28.13 - 42.19: 270 42.19 - 56.25: 99 56.25 - 70.32: 54 Dihedral angle restraints: 5859 sinusoidal: 1989 harmonic: 3870 Sorted by residual: dihedral pdb=" CA LYS X 34 " pdb=" CB LYS X 34 " pdb=" CG LYS X 34 " pdb=" CD LYS X 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.79 59.79 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS b 34 " pdb=" CB LYS b 34 " pdb=" CG LYS b 34 " pdb=" CD LYS b 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.76 59.76 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS L 34 " pdb=" CB LYS L 34 " pdb=" CG LYS L 34 " pdb=" CD LYS L 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.76 59.76 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 903 0.028 - 0.055: 415 0.055 - 0.083: 155 0.083 - 0.110: 169 0.110 - 0.138: 77 Chirality restraints: 1719 Sorted by residual: chirality pdb=" CA ILE L 88 " pdb=" N ILE L 88 " pdb=" C ILE L 88 " pdb=" CB ILE L 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE R 88 " pdb=" N ILE R 88 " pdb=" C ILE R 88 " pdb=" CB ILE R 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE V 88 " pdb=" N ILE V 88 " pdb=" C ILE V 88 " pdb=" CB ILE V 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1716 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU a 35 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" CD GLU a 35 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU a 35 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU a 35 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU Y 35 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.45e+00 pdb=" CD GLU Y 35 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU Y 35 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU Y 35 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU W 35 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" CD GLU W 35 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU W 35 " 0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU W 35 " 0.007 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 33 2.57 - 3.16: 7318 3.16 - 3.74: 14206 3.74 - 4.32: 20776 4.32 - 4.90: 40218 Nonbonded interactions: 82551 Sorted by model distance: nonbonded pdb=" CG2 VAL b 82 " pdb=" NE2 GLN P 24 " model vdw 1.993 3.540 nonbonded pdb=" CG2 VAL X 82 " pdb=" NE2 GLN b 24 " model vdw 1.993 3.540 nonbonded pdb=" CG2 VAL N 82 " pdb=" NE2 GLN T 24 " model vdw 1.993 3.540 nonbonded pdb=" CG2 VAL V 82 " pdb=" NE2 GLN Z 24 " model vdw 1.993 3.540 nonbonded pdb=" CG2 VAL R 82 " pdb=" NE2 GLN V 24 " model vdw 1.994 3.540 ... (remaining 82546 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: 0.09 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'b' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 0.970 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 9882 Z= 0.375 Angle : 0.586 6.224 13320 Z= 0.346 Chirality : 0.050 0.138 1719 Planarity : 0.002 0.012 1674 Dihedral : 18.156 70.318 3429 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.85 % Allowed : 18.52 % Favored : 79.63 % 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: -2.65 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS a 50 PHE 0.010 0.003 PHE Z 94 TYR 0.012 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.957 Fit side-chains REVERT: L 43 LYS cc_start: 0.8695 (mttt) cc_final: 0.8474 (mtpp) REVERT: L 100 LEU cc_start: 0.5043 (OUTLIER) cc_final: 0.4679 (mp) REVERT: N 45 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8224 (mttm) REVERT: Q 60 LYS cc_start: 0.7613 (tttp) cc_final: 0.7382 (ttmt) REVERT: Q 72 THR cc_start: 0.8535 (p) cc_final: 0.8253 (t) REVERT: R 34 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7127 (mtpt) REVERT: R 83 GLU cc_start: 0.6477 (mt-10) cc_final: 0.5923 (mt-10) REVERT: U 21 LYS cc_start: 0.7762 (mptt) cc_final: 0.7403 (mtpt) REVERT: U 65 ASN cc_start: 0.8615 (t0) cc_final: 0.8337 (t0) REVERT: W 43 LYS cc_start: 0.8401 (mttt) cc_final: 0.7950 (mtpt) REVERT: Y 20 GLU cc_start: 0.7071 (pm20) cc_final: 0.6720 (pm20) REVERT: a 79 GLN cc_start: 0.8458 (mt0) cc_final: 0.8236 (mt0) outliers start: 18 outliers final: 10 residues processed: 254 average time/residue: 0.2877 time to fit residues: 94.8829 Evaluate side-chains 201 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN S 79 GLN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 HIS Y 24 GLN a 24 GLN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085475 restraints weight = 13129.722| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.28 r_work: 0.3149 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9882 Z= 0.217 Angle : 0.497 8.678 13320 Z= 0.271 Chirality : 0.051 0.180 1719 Planarity : 0.002 0.018 1674 Dihedral : 5.237 58.196 1453 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.91 % Allowed : 16.98 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.20), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Z 50 PHE 0.009 0.002 PHE V 94 TYR 0.010 0.002 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.941 Fit side-chains REVERT: K 38 LEU cc_start: 0.8866 (pp) cc_final: 0.8438 (pp) REVERT: L 43 LYS cc_start: 0.8784 (mttt) cc_final: 0.8524 (mtpp) REVERT: L 100 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4963 (tt) REVERT: N 45 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8325 (mttm) REVERT: R 83 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6727 (mt-10) REVERT: U 38 LEU cc_start: 0.8770 (pp) cc_final: 0.8515 (pp) REVERT: V 34 LYS cc_start: 0.7571 (mttt) cc_final: 0.7320 (mttp) REVERT: W 21 LYS cc_start: 0.7449 (mtmt) cc_final: 0.7247 (mmtt) REVERT: X 83 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7253 (mm-30) REVERT: X 97 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8163 (mttt) REVERT: Y 83 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7546 (mt-10) REVERT: a 79 GLN cc_start: 0.8722 (mt0) cc_final: 0.8463 (mt0) REVERT: P 45 LYS cc_start: 0.8705 (mttt) cc_final: 0.8319 (mttm) outliers start: 38 outliers final: 15 residues processed: 212 average time/residue: 0.2496 time to fit residues: 70.9231 Evaluate side-chains 189 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 100 LEU Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain b residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 24 GLN ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079457 restraints weight = 13657.467| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.25 r_work: 0.3050 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 9882 Z= 0.454 Angle : 0.613 11.750 13320 Z= 0.326 Chirality : 0.052 0.183 1719 Planarity : 0.002 0.014 1674 Dihedral : 5.592 53.872 1447 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.73 % Allowed : 16.87 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 50 PHE 0.013 0.004 PHE V 94 TYR 0.018 0.002 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.943 Fit side-chains REVERT: L 43 LYS cc_start: 0.8742 (mttt) cc_final: 0.8488 (mtpp) REVERT: L 100 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.5001 (tt) REVERT: M 61 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: N 45 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8259 (mttm) REVERT: R 83 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6921 (mt-10) REVERT: S 57 GLU cc_start: 0.8048 (tt0) cc_final: 0.7776 (tt0) REVERT: U 38 LEU cc_start: 0.8891 (pp) cc_final: 0.8624 (pp) REVERT: U 61 GLU cc_start: 0.8589 (mp0) cc_final: 0.8250 (mt-10) REVERT: W 21 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7202 (mmtt) REVERT: X 83 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7255 (mm-30) REVERT: Z 83 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7528 (mt-10) REVERT: O 61 GLU cc_start: 0.8529 (mp0) cc_final: 0.8136 (mt-10) REVERT: P 21 LYS cc_start: 0.6490 (mttm) cc_final: 0.6231 (mttp) outliers start: 46 outliers final: 33 residues processed: 203 average time/residue: 0.2673 time to fit residues: 73.2230 Evaluate side-chains 209 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 GLN ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082416 restraints weight = 13423.073| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.30 r_work: 0.3111 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9882 Z= 0.209 Angle : 0.495 9.874 13320 Z= 0.265 Chirality : 0.050 0.137 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.164 56.839 1447 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.60 % Allowed : 19.03 % Favored : 77.37 % 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: -2.58 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS Z 50 PHE 0.009 0.002 PHE T 94 TYR 0.009 0.001 TYR U 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.318 Fit side-chains REVERT: K 38 LEU cc_start: 0.8819 (pp) cc_final: 0.8409 (pp) REVERT: K 61 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: L 43 LYS cc_start: 0.8722 (mttt) cc_final: 0.8434 (mtpp) REVERT: L 100 LEU cc_start: 0.5180 (OUTLIER) cc_final: 0.4945 (tt) REVERT: N 45 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8292 (mttm) REVERT: R 83 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6717 (mt-10) REVERT: U 38 LEU cc_start: 0.8822 (pp) cc_final: 0.8456 (pp) REVERT: W 21 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7160 (mmtt) REVERT: X 83 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7291 (mm-30) REVERT: a 28 GLU cc_start: 0.8244 (tt0) cc_final: 0.7830 (tt0) REVERT: a 61 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: b 95 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9041 (t) REVERT: O 21 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8203 (mptt) REVERT: O 61 GLU cc_start: 0.8488 (mp0) cc_final: 0.8143 (mt-10) outliers start: 35 outliers final: 21 residues processed: 196 average time/residue: 0.2577 time to fit residues: 68.1725 Evaluate side-chains 195 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 50 HIS ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.093098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077691 restraints weight = 13725.098| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.24 r_work: 0.3015 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 9882 Z= 0.658 Angle : 0.708 13.298 13320 Z= 0.377 Chirality : 0.055 0.166 1719 Planarity : 0.003 0.015 1674 Dihedral : 5.920 58.637 1447 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.45 % Allowed : 18.52 % Favored : 76.03 % 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: -2.85 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 50 PHE 0.017 0.005 PHE V 94 TYR 0.020 0.003 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.998 Fit side-chains REVERT: K 61 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: L 34 LYS cc_start: 0.8029 (mttt) cc_final: 0.7553 (mtpt) REVERT: L 35 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7528 (tt0) REVERT: L 43 LYS cc_start: 0.8779 (mttt) cc_final: 0.8463 (mtpp) REVERT: L 100 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.5059 (tt) REVERT: M 61 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: N 35 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: N 45 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8264 (mttp) REVERT: R 100 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5824 (tt) REVERT: T 35 GLU cc_start: 0.7978 (tt0) cc_final: 0.7776 (tt0) REVERT: U 61 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: W 21 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7273 (mmtt) REVERT: a 61 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: b 98 ASP cc_start: 0.8728 (m-30) cc_final: 0.8429 (m-30) REVERT: O 21 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8257 (mptt) REVERT: O 57 GLU cc_start: 0.8520 (tt0) cc_final: 0.8123 (tt0) REVERT: P 21 LYS cc_start: 0.6649 (mttm) cc_final: 0.6214 (mttp) outliers start: 53 outliers final: 36 residues processed: 207 average time/residue: 0.2539 time to fit residues: 70.4666 Evaluate side-chains 219 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085648 restraints weight = 13447.282| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.06 r_work: 0.3123 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9882 Z= 0.189 Angle : 0.503 10.878 13320 Z= 0.268 Chirality : 0.050 0.137 1719 Planarity : 0.002 0.011 1674 Dihedral : 5.265 53.710 1447 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.70 % Allowed : 20.68 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.66 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS Z 50 PHE 0.009 0.002 PHE X 94 TYR 0.008 0.001 TYR U 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.131 Fit side-chains REVERT: K 38 LEU cc_start: 0.8865 (pp) cc_final: 0.8449 (pp) REVERT: K 61 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: L 43 LYS cc_start: 0.8763 (mttt) cc_final: 0.8480 (mtpp) REVERT: L 100 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.5062 (tt) REVERT: N 45 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8259 (mttm) REVERT: R 83 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7251 (mm-30) REVERT: U 38 LEU cc_start: 0.8860 (pp) cc_final: 0.8472 (pp) REVERT: U 61 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: W 21 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7327 (mmtt) REVERT: a 28 GLU cc_start: 0.8177 (tt0) cc_final: 0.7771 (tt0) REVERT: a 61 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: b 95 VAL cc_start: 0.9418 (p) cc_final: 0.9045 (t) REVERT: O 21 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8250 (mptt) outliers start: 36 outliers final: 24 residues processed: 187 average time/residue: 0.2481 time to fit residues: 62.9076 Evaluate side-chains 189 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077002 restraints weight = 13993.428| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.28 r_work: 0.3016 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.056 9882 Z= 0.661 Angle : 0.716 13.588 13320 Z= 0.381 Chirality : 0.055 0.160 1719 Planarity : 0.003 0.016 1674 Dihedral : 5.900 57.848 1447 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.42 % Allowed : 20.47 % Favored : 75.10 % 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: -2.90 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS b 50 PHE 0.018 0.005 PHE R 94 TYR 0.019 0.003 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 1.077 Fit side-chains REVERT: K 61 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: L 34 LYS cc_start: 0.8020 (mttt) cc_final: 0.7542 (mtpt) REVERT: L 35 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7546 (tt0) REVERT: L 43 LYS cc_start: 0.8764 (mttt) cc_final: 0.8440 (mtpp) REVERT: L 100 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5111 (tt) REVERT: M 61 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: N 35 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: N 45 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8264 (mttp) REVERT: Q 60 LYS cc_start: 0.8014 (tttp) cc_final: 0.7462 (ttmt) REVERT: R 100 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5872 (tt) REVERT: U 61 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: W 21 LYS cc_start: 0.7632 (mtmt) cc_final: 0.7280 (mmtt) REVERT: a 61 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8526 (mp0) REVERT: b 98 ASP cc_start: 0.8731 (m-30) cc_final: 0.8403 (m-30) REVERT: O 57 GLU cc_start: 0.8493 (tt0) cc_final: 0.8122 (tt0) REVERT: P 21 LYS cc_start: 0.6631 (mttm) cc_final: 0.6007 (mttp) outliers start: 43 outliers final: 32 residues processed: 201 average time/residue: 0.2538 time to fit residues: 68.5266 Evaluate side-chains 211 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 80 LYS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081535 restraints weight = 13503.794| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.27 r_work: 0.3091 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9882 Z= 0.209 Angle : 0.525 11.430 13320 Z= 0.278 Chirality : 0.050 0.140 1719 Planarity : 0.002 0.011 1674 Dihedral : 5.321 53.187 1447 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.70 % Allowed : 22.12 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Z 50 PHE 0.010 0.002 PHE X 94 TYR 0.008 0.002 TYR U 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.539 Fit side-chains REVERT: K 38 LEU cc_start: 0.8852 (pp) cc_final: 0.8445 (pp) REVERT: K 61 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: L 43 LYS cc_start: 0.8733 (mttt) cc_final: 0.8430 (mtpp) REVERT: L 100 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4954 (tt) REVERT: N 100 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5229 (tt) REVERT: U 61 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: W 21 LYS cc_start: 0.7569 (mtmt) cc_final: 0.7198 (mmtt) REVERT: Y 65 ASN cc_start: 0.9004 (t0) cc_final: 0.8786 (t0) REVERT: Z 35 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: a 61 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: b 95 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9028 (t) REVERT: b 98 ASP cc_start: 0.8625 (m-30) cc_final: 0.8202 (m-30) REVERT: O 21 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8229 (mptt) outliers start: 36 outliers final: 22 residues processed: 189 average time/residue: 0.2385 time to fit residues: 61.8558 Evaluate side-chains 198 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079070 restraints weight = 13760.579| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.30 r_work: 0.3054 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9882 Z= 0.389 Angle : 0.607 13.051 13320 Z= 0.318 Chirality : 0.051 0.144 1719 Planarity : 0.002 0.027 1674 Dihedral : 5.506 55.333 1447 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.22 % Allowed : 21.40 % Favored : 74.38 % 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: -2.73 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 50 PHE 0.013 0.003 PHE X 94 TYR 0.014 0.002 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.946 Fit side-chains REVERT: K 61 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: L 43 LYS cc_start: 0.8754 (mttt) cc_final: 0.8467 (mtpp) REVERT: L 100 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.5005 (tt) REVERT: N 35 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: N 100 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5377 (tt) REVERT: Q 60 LYS cc_start: 0.7997 (tttp) cc_final: 0.7471 (ttmt) REVERT: U 38 LEU cc_start: 0.8824 (pp) cc_final: 0.8624 (pp) REVERT: U 61 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: W 21 LYS cc_start: 0.7644 (mtmt) cc_final: 0.7309 (mmtt) REVERT: Z 35 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: b 35 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: b 98 ASP cc_start: 0.8657 (m-30) cc_final: 0.8299 (m-30) REVERT: P 21 LYS cc_start: 0.6642 (mttm) cc_final: 0.5884 (mttp) outliers start: 41 outliers final: 29 residues processed: 193 average time/residue: 0.2341 time to fit residues: 61.6259 Evaluate side-chains 208 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 23 LYS Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083578 restraints weight = 13514.691| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.30 r_work: 0.3131 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9882 Z= 0.141 Angle : 0.499 11.495 13320 Z= 0.262 Chirality : 0.050 0.133 1719 Planarity : 0.001 0.013 1674 Dihedral : 4.939 47.671 1447 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.78 % Allowed : 23.15 % Favored : 74.07 % 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: -2.53 (0.20), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Z 50 PHE 0.008 0.002 PHE X 94 TYR 0.006 0.001 TYR U 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.974 Fit side-chains REVERT: K 38 LEU cc_start: 0.8818 (pp) cc_final: 0.8445 (pp) REVERT: L 43 LYS cc_start: 0.8697 (mttt) cc_final: 0.8418 (mtpp) REVERT: L 100 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4960 (tt) REVERT: N 59 THR cc_start: 0.8998 (m) cc_final: 0.8778 (p) REVERT: W 21 LYS cc_start: 0.7579 (mtmt) cc_final: 0.7224 (mmtt) REVERT: Z 35 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: b 35 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: b 95 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.8989 (t) REVERT: O 61 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8118 (mt-10) REVERT: P 83 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6870 (tm-30) outliers start: 27 outliers final: 18 residues processed: 178 average time/residue: 0.2414 time to fit residues: 58.8256 Evaluate side-chains 181 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.077803 restraints weight = 13868.459| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.30 r_work: 0.3027 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 9882 Z= 0.560 Angle : 0.674 13.833 13320 Z= 0.354 Chirality : 0.053 0.192 1719 Planarity : 0.003 0.016 1674 Dihedral : 5.522 56.092 1445 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.88 % Allowed : 22.63 % 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: -2.76 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS b 50 PHE 0.016 0.004 PHE R 94 TYR 0.019 0.003 TYR U 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.25 seconds wall clock time: 77 minutes 12.60 seconds (4632.60 seconds total)