Starting phenix.real_space_refine on Fri Feb 14 02:08:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cda_45465/02_2025/9cda_45465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cda_45465/02_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_45465/02_2025/9cda_45465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cda_45465/02_2025/9cda_45465.map" model { file = "/net/cci-nas-00/data/ceres_data/9cda_45465/02_2025/9cda_45465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cda_45465/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.28, per 1000 atoms: 0.33 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 1.23 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: 2.53 Time building geometry restraints manager: 2.76 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: 0.08 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: 1.180 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: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 21.250 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- 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 : 1.093 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: 0.2941 time to fit residues: 97.1370 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 : 1.023 ------------------------------------------------------------------------------- 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 = 13129.723| |-----------------------------------------------------------------------------| 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: 0.8673 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 : 1.020 Fit side-chains REVERT: K 38 LEU cc_start: 0.8866 (pp) cc_final: 0.8437 (pp) REVERT: L 43 LYS cc_start: 0.8783 (mttt) cc_final: 0.8522 (mtpp) REVERT: L 100 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4963 (tt) REVERT: N 45 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8326 (mttm) REVERT: R 83 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6733 (mt-10) REVERT: U 38 LEU cc_start: 0.8770 (pp) cc_final: 0.8516 (pp) REVERT: V 34 LYS cc_start: 0.7573 (mttt) cc_final: 0.7320 (mttp) REVERT: W 21 LYS cc_start: 0.7445 (mtmt) cc_final: 0.7241 (mmtt) REVERT: X 83 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7256 (mm-30) REVERT: X 97 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8162 (mttt) REVERT: Y 83 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7544 (mt-10) REVERT: a 79 GLN cc_start: 0.8721 (mt0) cc_final: 0.8462 (mt0) REVERT: P 45 LYS cc_start: 0.8705 (mttt) cc_final: 0.8320 (mttm) outliers start: 38 outliers final: 15 residues processed: 212 average time/residue: 0.2669 time to fit residues: 76.2278 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 : 1.156 ------------------------------------------------------------------------------- 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: 7.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.094939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079313 restraints weight = 13696.221| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.24 r_work: 0.3038 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 9882 Z= 0.525 Angle : 0.648 11.738 13320 Z= 0.345 Chirality : 0.053 0.189 1719 Planarity : 0.003 0.014 1674 Dihedral : 5.759 56.149 1447 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.84 % Allowed : 16.67 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Z 50 PHE 0.014 0.004 PHE V 94 TYR 0.019 0.003 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 230 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 1.036 Fit side-chains REVERT: K 61 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: L 34 LYS cc_start: 0.7995 (mttt) cc_final: 0.7507 (mtpt) REVERT: L 43 LYS cc_start: 0.8759 (mttt) cc_final: 0.8445 (mtpp) REVERT: M 61 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: N 45 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8238 (mttm) REVERT: R 83 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6922 (mt-10) REVERT: S 61 GLU cc_start: 0.8738 (mp0) cc_final: 0.8340 (mm-30) REVERT: U 38 LEU cc_start: 0.8934 (pp) cc_final: 0.8674 (pp) REVERT: W 21 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7215 (mmtt) REVERT: X 83 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7204 (mm-30) REVERT: Z 83 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7555 (mt-10) REVERT: O 61 GLU cc_start: 0.8593 (mp0) cc_final: 0.8110 (mt-10) REVERT: P 21 LYS cc_start: 0.6516 (mttm) cc_final: 0.6181 (mttp) REVERT: P 83 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7213 (tm-30) outliers start: 47 outliers final: 33 residues processed: 210 average time/residue: 0.2538 time to fit residues: 71.5329 Evaluate side-chains 214 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 83 GLU 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: 0.0060 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.097814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081898 restraints weight = 13505.679| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.27 r_work: 0.3099 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9882 Z= 0.235 Angle : 0.517 10.155 13320 Z= 0.274 Chirality : 0.050 0.140 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.197 58.271 1445 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.70 % Allowed : 19.86 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS Z 50 PHE 0.010 0.002 PHE X 94 TYR 0.010 0.002 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 213 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.011 Fit side-chains REVERT: K 38 LEU cc_start: 0.8853 (pp) cc_final: 0.8429 (pp) REVERT: L 43 LYS cc_start: 0.8740 (mttt) cc_final: 0.8444 (mtpp) REVERT: N 45 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8283 (mttm) REVERT: R 83 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6744 (mt-10) REVERT: W 21 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7205 (mmtt) REVERT: X 83 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7305 (mm-30) REVERT: a 28 GLU cc_start: 0.8248 (tt0) cc_final: 0.7842 (tt0) REVERT: a 61 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: b 95 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9050 (t) REVERT: O 21 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8246 (mptt) REVERT: O 61 GLU cc_start: 0.8576 (mp0) cc_final: 0.8152 (mt-10) outliers start: 36 outliers final: 22 residues processed: 193 average time/residue: 0.2443 time to fit residues: 63.8906 Evaluate side-chains 192 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR 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 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: 6.9990 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 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: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 50 HIS ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077448 restraints weight = 13770.108| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.24 r_work: 0.3009 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.066 9882 Z= 0.753 Angle : 0.763 13.478 13320 Z= 0.406 Chirality : 0.057 0.179 1719 Planarity : 0.003 0.015 1674 Dihedral : 5.945 59.096 1445 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.84 % Allowed : 19.75 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.93 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 50 PHE 0.019 0.005 PHE R 94 TYR 0.021 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 231 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.985 Fit side-chains REVERT: L 34 LYS cc_start: 0.8042 (mttt) cc_final: 0.7566 (mtpt) REVERT: L 35 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7574 (tt0) REVERT: L 43 LYS cc_start: 0.8797 (mttt) cc_final: 0.8473 (mtpp) REVERT: M 61 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: N 35 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: N 43 LYS cc_start: 0.8923 (mttt) cc_final: 0.8658 (mttt) REVERT: N 45 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8278 (mttp) REVERT: Q 60 LYS cc_start: 0.8010 (tttp) cc_final: 0.7501 (ttmt) REVERT: R 100 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5930 (tt) REVERT: U 61 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: W 21 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7268 (mmtt) REVERT: Y 20 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: a 61 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: b 98 ASP cc_start: 0.8755 (m-30) cc_final: 0.8457 (m-30) REVERT: P 21 LYS cc_start: 0.6651 (mttm) cc_final: 0.6034 (mttp) outliers start: 47 outliers final: 33 residues processed: 205 average time/residue: 0.2582 time to fit residues: 70.9095 Evaluate side-chains 217 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 81 THR Chi-restraints excluded: chain R residue 100 LEU 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: 1.9990 chunk 38 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.098052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082248 restraints weight = 13318.966| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.25 r_work: 0.3115 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9882 Z= 0.175 Angle : 0.502 10.634 13320 Z= 0.267 Chirality : 0.050 0.136 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.153 54.378 1445 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.50 % Allowed : 22.02 % 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: -2.67 (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 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 214 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.112 Fit side-chains REVERT: K 38 LEU cc_start: 0.8825 (pp) cc_final: 0.8412 (pp) REVERT: L 43 LYS cc_start: 0.8742 (mttt) cc_final: 0.8464 (mtpp) REVERT: N 34 LYS cc_start: 0.8070 (mttt) cc_final: 0.7371 (mtpt) REVERT: N 35 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: N 43 LYS cc_start: 0.8868 (mttt) cc_final: 0.8612 (mttt) REVERT: N 45 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8239 (mttm) REVERT: R 83 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7274 (mm-30) REVERT: U 38 LEU cc_start: 0.8806 (pp) cc_final: 0.8566 (pp) REVERT: U 61 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: W 21 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7166 (mmtt) REVERT: Y 65 ASN cc_start: 0.9011 (t0) cc_final: 0.8796 (t0) REVERT: a 28 GLU cc_start: 0.8210 (tt0) cc_final: 0.7810 (tt0) REVERT: a 61 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: b 95 VAL cc_start: 0.9407 (p) cc_final: 0.9032 (t) REVERT: O 21 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8232 (mptt) outliers start: 34 outliers final: 21 residues processed: 194 average time/residue: 0.2553 time to fit residues: 66.7149 Evaluate side-chains 192 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 81 THR 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 75 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 X residue 97 LYS Chi-restraints excluded: chain Y residue 81 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: 0.0020 chunk 74 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 143 optimal weight: 0.0010 chunk 58 optimal weight: 0.6980 overall best weight: 2.5398 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.094924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079024 restraints weight = 13844.077| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.31 r_work: 0.3049 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9882 Z= 0.398 Angle : 0.590 12.729 13320 Z= 0.311 Chirality : 0.051 0.145 1719 Planarity : 0.002 0.015 1674 Dihedral : 5.417 56.452 1445 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.12 % Allowed : 21.71 % 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: -2.74 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (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 R 94 TYR 0.015 0.002 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 220 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.011 Fit side-chains REVERT: L 43 LYS cc_start: 0.8764 (mttt) cc_final: 0.8489 (mtpp) REVERT: N 35 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: N 45 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8304 (mttp) REVERT: R 83 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7333 (mm-30) REVERT: R 100 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5870 (tt) REVERT: U 38 LEU cc_start: 0.8871 (pp) cc_final: 0.8659 (pp) REVERT: U 61 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: W 21 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7308 (mmtt) REVERT: Z 35 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: b 35 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: b 98 ASP cc_start: 0.8681 (m-30) cc_final: 0.8315 (m-30) REVERT: O 21 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8295 (mptt) REVERT: P 21 LYS cc_start: 0.6627 (mttm) cc_final: 0.6003 (mttp) outliers start: 40 outliers final: 30 residues processed: 200 average time/residue: 0.2531 time to fit residues: 68.3998 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 : 1.071 ------------------------------------------------------------------------------- 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 M residue 33 THR 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 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 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 33 THR Chi-restraints excluded: chain a residue 81 THR 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 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: 0.6980 chunk 120 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.094679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078807 restraints weight = 13844.515| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.30 r_work: 0.3035 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 9882 Z= 0.456 Angle : 0.639 12.808 13320 Z= 0.338 Chirality : 0.052 0.147 1719 Planarity : 0.002 0.024 1674 Dihedral : 5.560 58.716 1445 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.32 % Allowed : 22.12 % Favored : 73.56 % 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: -2.80 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 50 PHE 0.014 0.004 PHE X 94 TYR 0.015 0.003 TYR Y 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 214 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.994 Fit side-chains REVERT: L 43 LYS cc_start: 0.8726 (mttt) cc_final: 0.8418 (mtpp) REVERT: L 100 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.5195 (tt) REVERT: M 61 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: N 35 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: N 100 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.5348 (tt) REVERT: Q 60 LYS cc_start: 0.7951 (tttp) cc_final: 0.7436 (ttmt) REVERT: R 83 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7355 (mm-30) REVERT: R 100 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5958 (tt) REVERT: U 38 LEU cc_start: 0.8859 (pp) cc_final: 0.8653 (pp) REVERT: U 61 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: W 21 LYS cc_start: 0.7563 (mtmt) cc_final: 0.7199 (mmtt) REVERT: Z 35 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: b 35 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: b 98 ASP cc_start: 0.8683 (m-30) cc_final: 0.8304 (m-30) REVERT: P 21 LYS cc_start: 0.6608 (mttm) cc_final: 0.5989 (mttp) outliers start: 42 outliers final: 30 residues processed: 194 average time/residue: 0.2430 time to fit residues: 64.3027 Evaluate side-chains 208 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.097763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082871 restraints weight = 13829.052| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.08 r_work: 0.3062 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9882 Z= 0.412 Angle : 0.617 12.858 13320 Z= 0.324 Chirality : 0.052 0.146 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.514 59.512 1445 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.42 % Allowed : 22.12 % Favored : 73.46 % 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: -2.79 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 50 PHE 0.014 0.004 PHE X 94 TYR 0.014 0.002 TYR U 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 218 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.013 Fit side-chains REVERT: K 38 LEU cc_start: 0.8931 (pp) cc_final: 0.8490 (pp) REVERT: L 43 LYS cc_start: 0.8789 (mttt) cc_final: 0.8520 (mtpp) REVERT: L 100 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5251 (tt) REVERT: M 61 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: N 35 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: N 100 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5569 (tt) REVERT: Q 60 LYS cc_start: 0.8078 (tttp) cc_final: 0.7571 (ttmt) REVERT: R 83 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7321 (mm-30) REVERT: R 100 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6070 (tt) REVERT: U 38 LEU cc_start: 0.8893 (pp) cc_final: 0.8673 (pp) REVERT: U 61 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: W 21 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7413 (mmtt) REVERT: X 97 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8393 (mttt) REVERT: Z 35 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: a 61 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8184 (mt-10) REVERT: b 35 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: b 98 ASP cc_start: 0.8659 (m-30) cc_final: 0.8346 (m-30) REVERT: P 21 LYS cc_start: 0.6702 (mttm) cc_final: 0.5945 (mttp) outliers start: 43 outliers final: 30 residues processed: 197 average time/residue: 0.2517 time to fit residues: 67.6259 Evaluate side-chains 213 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 81 THR Chi-restraints excluded: chain X residue 97 LYS 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 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: 0.9990 chunk 108 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 95 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** b 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083163 restraints weight = 13582.567| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.23 r_work: 0.3118 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9882 Z= 0.150 Angle : 0.500 11.554 13320 Z= 0.263 Chirality : 0.050 0.134 1719 Planarity : 0.001 0.016 1674 Dihedral : 4.967 52.852 1445 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.19 % Allowed : 23.25 % Favored : 73.56 % 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: -2.57 (0.20), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (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 0.007 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 201 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.217 Fit side-chains REVERT: K 38 LEU cc_start: 0.8843 (pp) cc_final: 0.8457 (pp) REVERT: L 43 LYS cc_start: 0.8725 (mttt) cc_final: 0.8455 (mtpp) REVERT: L 100 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5209 (tt) REVERT: M 61 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: N 35 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: R 83 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7198 (mm-30) REVERT: U 38 LEU cc_start: 0.8765 (pp) cc_final: 0.8534 (pp) REVERT: W 21 LYS cc_start: 0.7612 (mtmt) cc_final: 0.7231 (mmtt) REVERT: X 97 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8227 (mttt) REVERT: Y 20 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: a 28 GLU cc_start: 0.8228 (tt0) cc_final: 0.7821 (tt0) REVERT: a 61 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8248 (mt-10) REVERT: b 95 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9021 (t) REVERT: b 98 ASP cc_start: 0.8539 (m-30) cc_final: 0.8163 (m-30) outliers start: 31 outliers final: 19 residues processed: 184 average time/residue: 0.2353 time to fit residues: 59.5166 Evaluate side-chains 187 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR 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 61 GLU Chi-restraints excluded: chain N residue 35 GLU 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 87 SER Chi-restraints excluded: chain W residue 88 ILE 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 81 THR 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: 1.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 143 optimal weight: 0.0870 overall best weight: 1.7362 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.096100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080601 restraints weight = 13709.941| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.16 r_work: 0.3083 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9882 Z= 0.285 Angle : 0.547 12.486 13320 Z= 0.287 Chirality : 0.050 0.151 1719 Planarity : 0.002 0.011 1674 Dihedral : 4.998 53.536 1443 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.09 % Allowed : 22.33 % Favored : 74.59 % 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 (0.20), 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 0.012 0.003 PHE X 94 TYR 0.013 0.002 TYR U 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.46 seconds wall clock time: 78 minutes 2.31 seconds (4682.31 seconds total)