Starting phenix.real_space_refine on Wed Sep 17 16:13:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cda_45465/09_2025/9cda_45465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cda_45465/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cda_45465/09_2025/9cda_45465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cda_45465/09_2025/9cda_45465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cda_45465/09_2025/9cda_45465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cda_45465/09_2025/9cda_45465.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 2 Chain: "K" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 538 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "L" 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: M, Q, S, U, W, Y, a, O, N, R, T, V, X, Z, b, P Time building chain proxies: 1.21, per 1000 atoms: 0.12 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: 0.91 Conformation dependent library (CDL) restraints added in 408.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.43 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: 1.63 Time building geometry restraints manager: 1.13 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: 0.02 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'P' } 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- 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= 0.242 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.012 0.002 TYR O 39 PHE 0.010 0.003 PHE Z 94 HIS 0.001 0.000 HIS a 50 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 9882) covalent geometry : angle 0.58590 (13320) hydrogen bonds : bond 0.17984 ( 196) hydrogen bonds : angle 7.51644 ( 588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.379 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: 0.1384 time to fit residues: 45.7090 Evaluate side-chains 201 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** Q 24 GLN S 79 GLN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 HIS Y 24 GLN ** Z 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 24 GLN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080035 restraints weight = 13809.862| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.28 r_work: 0.3029 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 9882 Z= 0.373 Angle : 0.698 11.060 13320 Z= 0.377 Chirality : 0.055 0.204 1719 Planarity : 0.003 0.019 1674 Dihedral : 6.601 55.435 1453 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.73 % Allowed : 17.28 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.019 0.003 TYR Y 39 PHE 0.015 0.004 PHE V 94 HIS 0.005 0.001 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00898 ( 9882) covalent geometry : angle 0.69798 (13320) hydrogen bonds : bond 0.03079 ( 196) hydrogen bonds : angle 5.77282 ( 588) *********************** 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 241 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.386 Fit side-chains REVERT: L 34 LYS cc_start: 0.8020 (mttt) cc_final: 0.7540 (mtpt) REVERT: L 43 LYS cc_start: 0.8788 (mttt) cc_final: 0.8478 (mtpp) REVERT: L 100 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4989 (tt) REVERT: M 61 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: N 45 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8342 (mttp) REVERT: Q 72 THR cc_start: 0.8669 (p) cc_final: 0.8349 (t) REVERT: R 83 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6715 (mt-10) REVERT: U 38 LEU cc_start: 0.8937 (pp) cc_final: 0.8691 (pp) REVERT: W 21 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7261 (mmtt) REVERT: W 38 LEU cc_start: 0.8900 (pp) cc_final: 0.8601 (pp) REVERT: Y 23 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7994 (mmmt) REVERT: O 61 GLU cc_start: 0.8581 (mp0) cc_final: 0.8098 (mt-10) REVERT: P 21 LYS cc_start: 0.6514 (mttm) cc_final: 0.6245 (mttp) outliers start: 46 outliers final: 31 residues processed: 219 average time/residue: 0.1161 time to fit residues: 34.1928 Evaluate side-chains 216 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 100 LEU 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 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 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 80 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083876 restraints weight = 13357.818| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.30 r_work: 0.3129 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9882 Z= 0.097 Angle : 0.463 8.450 13320 Z= 0.250 Chirality : 0.050 0.150 1719 Planarity : 0.002 0.014 1674 Dihedral : 5.679 56.391 1453 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.32 % Allowed : 17.90 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR U 39 PHE 0.007 0.002 PHE T 94 HIS 0.002 0.001 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9882) covalent geometry : angle 0.46297 (13320) hydrogen bonds : bond 0.01576 ( 196) hydrogen bonds : angle 4.84439 ( 588) *********************** 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 224 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.382 Fit side-chains REVERT: K 38 LEU cc_start: 0.8821 (pp) cc_final: 0.8362 (pp) REVERT: L 43 LYS cc_start: 0.8742 (mttt) cc_final: 0.8450 (mtpp) REVERT: L 100 LEU cc_start: 0.5256 (OUTLIER) cc_final: 0.5020 (tt) REVERT: N 35 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: N 45 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8291 (mttm) REVERT: R 83 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6734 (mt-10) REVERT: U 38 LEU cc_start: 0.8816 (pp) cc_final: 0.8532 (pp) REVERT: W 21 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7198 (mmtt) REVERT: X 83 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7257 (mm-30) REVERT: Y 21 LYS cc_start: 0.8503 (mttp) cc_final: 0.8302 (mmtt) REVERT: Y 65 ASN cc_start: 0.8782 (t0) cc_final: 0.8564 (t0) REVERT: a 28 GLU cc_start: 0.8194 (tt0) cc_final: 0.7780 (tt0) REVERT: a 61 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: b 95 VAL cc_start: 0.9395 (p) cc_final: 0.9058 (t) REVERT: O 21 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8145 (mptt) REVERT: O 60 LYS cc_start: 0.8076 (tttt) cc_final: 0.7697 (tttm) outliers start: 42 outliers final: 17 residues processed: 205 average time/residue: 0.1105 time to fit residues: 30.6225 Evaluate side-chains 190 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 75 THR 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 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 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 61 GLU Chi-restraints excluded: chain a residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 Q 79 GLN S 24 GLN V 50 HIS ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.092425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076948 restraints weight = 14080.483| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.27 r_work: 0.3003 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.073 9882 Z= 0.444 Angle : 0.746 14.593 13320 Z= 0.395 Chirality : 0.057 0.169 1719 Planarity : 0.003 0.015 1674 Dihedral : 6.671 59.559 1452 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 5.25 % Allowed : 19.03 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR Y 39 PHE 0.018 0.005 PHE R 94 HIS 0.002 0.001 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.01068 ( 9882) covalent geometry : angle 0.74607 (13320) hydrogen bonds : bond 0.02715 ( 196) hydrogen bonds : angle 5.38595 ( 588) *********************** 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 241 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.369 Fit side-chains REVERT: K 61 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: L 34 LYS cc_start: 0.8033 (mttt) cc_final: 0.7554 (mtpt) REVERT: L 35 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7533 (tt0) REVERT: L 43 LYS cc_start: 0.8793 (mttt) cc_final: 0.8477 (mtpp) REVERT: L 100 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.5100 (tt) REVERT: M 61 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: N 35 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: N 43 LYS cc_start: 0.8943 (mttt) cc_final: 0.8664 (mttt) REVERT: N 45 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8294 (mttp) REVERT: Q 60 LYS cc_start: 0.7987 (tttp) cc_final: 0.7491 (ttmt) REVERT: U 61 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: W 21 LYS cc_start: 0.7593 (mtmt) cc_final: 0.7228 (mmtt) REVERT: a 61 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: b 98 ASP cc_start: 0.8726 (m-30) cc_final: 0.8429 (m-30) REVERT: P 21 LYS cc_start: 0.6582 (mttm) cc_final: 0.6138 (mttp) outliers start: 51 outliers final: 35 residues processed: 216 average time/residue: 0.1140 time to fit residues: 33.3695 Evaluate side-chains 221 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** b 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085468 restraints weight = 13507.768| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.09 r_work: 0.3127 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3124 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= 0.113 Angle : 0.497 10.682 13320 Z= 0.263 Chirality : 0.050 0.136 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.875 56.697 1452 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.60 % Allowed : 22.12 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR U 39 PHE 0.008 0.002 PHE T 94 HIS 0.002 0.001 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9882) covalent geometry : angle 0.49706 (13320) hydrogen bonds : bond 0.01456 ( 196) hydrogen bonds : angle 4.69923 ( 588) *********************** 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 212 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.376 Fit side-chains REVERT: K 38 LEU cc_start: 0.8832 (pp) cc_final: 0.8433 (pp) REVERT: K 61 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: L 43 LYS cc_start: 0.8792 (mttt) cc_final: 0.8532 (mtpp) REVERT: L 100 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.5111 (tt) REVERT: N 35 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: N 45 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8290 (mttm) REVERT: R 83 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7223 (mm-30) REVERT: R 100 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5573 (tt) REVERT: U 38 LEU cc_start: 0.8819 (pp) cc_final: 0.8471 (pp) REVERT: U 61 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: W 21 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7301 (mmtt) REVERT: a 28 GLU cc_start: 0.8222 (tt0) cc_final: 0.7828 (tt0) REVERT: a 61 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: b 95 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9050 (t) REVERT: O 61 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7906 (mt-10) outliers start: 35 outliers final: 20 residues processed: 192 average time/residue: 0.1193 time to fit residues: 30.7580 Evaluate side-chains 194 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain 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 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 23 LYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 135 optimal weight: 0.0980 overall best weight: 0.6282 ------------------------------------------------------------------------------- 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 79 GLN ** 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 = 0.3488 r_free = 0.3488 target = 0.102836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087770 restraints weight = 13505.466| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.10 r_work: 0.3161 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9882 Z= 0.091 Angle : 0.467 11.021 13320 Z= 0.247 Chirality : 0.050 0.133 1719 Planarity : 0.001 0.011 1674 Dihedral : 5.300 58.332 1452 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.50 % Allowed : 22.53 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.20), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR U 39 PHE 0.008 0.002 PHE R 94 HIS 0.002 0.001 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 9882) covalent geometry : angle 0.46748 (13320) hydrogen bonds : bond 0.01223 ( 196) hydrogen bonds : angle 4.41300 ( 588) *********************** 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 209 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.263 Fit side-chains REVERT: K 38 LEU cc_start: 0.8832 (pp) cc_final: 0.8496 (pp) REVERT: K 58 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8024 (mmtm) REVERT: L 43 LYS cc_start: 0.8722 (mttt) cc_final: 0.8484 (mtpp) REVERT: L 97 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8237 (mmtm) REVERT: L 100 LEU cc_start: 0.5474 (OUTLIER) cc_final: 0.5215 (tt) REVERT: N 34 LYS cc_start: 0.8110 (mttt) cc_final: 0.7442 (mtpt) REVERT: N 35 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: N 43 LYS cc_start: 0.8869 (mttt) cc_final: 0.8614 (mttt) REVERT: N 45 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8255 (mttm) REVERT: R 100 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5621 (tt) REVERT: S 61 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8169 (mt-10) REVERT: U 38 LEU cc_start: 0.8797 (pp) cc_final: 0.8479 (pp) REVERT: W 21 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7356 (mmtt) REVERT: a 28 GLU cc_start: 0.8222 (tt0) cc_final: 0.7844 (tt0) REVERT: b 95 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9003 (t) REVERT: O 61 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7922 (mt-10) outliers start: 34 outliers final: 20 residues processed: 193 average time/residue: 0.1220 time to fit residues: 31.6684 Evaluate side-chains 189 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 75 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 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 Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 79 GLN ** 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 = 0.3404 r_free = 0.3404 target = 0.097462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082527 restraints weight = 13789.574| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.09 r_work: 0.3072 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9882 Z= 0.234 Angle : 0.580 12.199 13320 Z= 0.307 Chirality : 0.051 0.159 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.567 51.204 1449 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.70 % Allowed : 22.43 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR Y 39 PHE 0.014 0.003 PHE R 94 HIS 0.001 0.000 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 9882) covalent geometry : angle 0.57966 (13320) hydrogen bonds : bond 0.01781 ( 196) hydrogen bonds : angle 4.87213 ( 588) *********************** 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 219 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.406 Fit side-chains REVERT: K 38 LEU cc_start: 0.8919 (pp) cc_final: 0.8504 (pp) REVERT: K 61 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: L 43 LYS cc_start: 0.8783 (mttt) cc_final: 0.8529 (mtpp) REVERT: L 100 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.5044 (tt) REVERT: N 35 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: N 43 LYS cc_start: 0.8911 (mttt) cc_final: 0.8651 (mttt) REVERT: N 45 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8366 (mttp) REVERT: R 100 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5751 (tt) REVERT: U 38 LEU cc_start: 0.8850 (pp) cc_final: 0.8584 (pp) REVERT: W 21 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7362 (mmtt) REVERT: a 61 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8172 (mt-10) REVERT: b 98 ASP cc_start: 0.8620 (m-30) cc_final: 0.8231 (m-30) REVERT: P 21 LYS cc_start: 0.6608 (mttm) cc_final: 0.6168 (mttp) outliers start: 36 outliers final: 26 residues processed: 198 average time/residue: 0.1200 time to fit residues: 31.9156 Evaluate side-chains 209 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 79 GLN ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.080277 restraints weight = 13610.602| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.15 r_work: 0.3079 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9882 Z= 0.206 Angle : 0.571 12.195 13320 Z= 0.301 Chirality : 0.051 0.143 1719 Planarity : 0.002 0.024 1674 Dihedral : 5.537 51.794 1449 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.81 % Allowed : 22.12 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR U 39 PHE 0.012 0.003 PHE R 94 HIS 0.002 0.000 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9882) covalent geometry : angle 0.57095 (13320) hydrogen bonds : bond 0.01706 ( 196) hydrogen bonds : angle 4.79938 ( 588) *********************** 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 217 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.400 Fit side-chains REVERT: K 38 LEU cc_start: 0.8904 (pp) cc_final: 0.8497 (pp) REVERT: K 61 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: L 43 LYS cc_start: 0.8754 (mttt) cc_final: 0.8497 (mtpp) REVERT: L 100 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5005 (tt) REVERT: N 35 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: N 45 LYS cc_start: 0.8848 (mtpt) cc_final: 0.8363 (mttp) REVERT: R 100 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5807 (tt) REVERT: W 21 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7282 (mmtt) REVERT: Z 35 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: a 61 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8198 (mt-10) REVERT: b 95 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9049 (t) REVERT: b 98 ASP cc_start: 0.8606 (m-30) cc_final: 0.8193 (m-30) outliers start: 37 outliers final: 26 residues processed: 197 average time/residue: 0.1225 time to fit residues: 32.5941 Evaluate side-chains 205 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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** W 79 GLN ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076620 restraints weight = 14034.120| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.29 r_work: 0.3006 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 9882 Z= 0.425 Angle : 0.750 13.899 13320 Z= 0.398 Chirality : 0.056 0.183 1719 Planarity : 0.003 0.014 1674 Dihedral : 6.156 59.938 1449 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 4.01 % Allowed : 22.22 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR Y 39 PHE 0.019 0.005 PHE V 94 HIS 0.003 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.01024 ( 9882) covalent geometry : angle 0.75049 (13320) hydrogen bonds : bond 0.02566 ( 196) hydrogen bonds : angle 5.25532 ( 588) *********************** 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 219 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.382 Fit side-chains REVERT: K 61 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: L 35 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7547 (tt0) REVERT: L 43 LYS cc_start: 0.8752 (mttt) cc_final: 0.8448 (mtpp) REVERT: L 100 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4972 (tt) REVERT: M 43 LYS cc_start: 0.8611 (mttt) cc_final: 0.8170 (mttm) REVERT: N 35 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: N 100 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5474 (tt) REVERT: Q 60 LYS cc_start: 0.8036 (tttp) cc_final: 0.7494 (ttmt) REVERT: R 97 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7983 (mmtp) REVERT: R 100 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6077 (tt) REVERT: W 21 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7305 (mmtt) REVERT: X 97 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: Z 35 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: a 61 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8260 (mt-10) REVERT: b 35 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: b 98 ASP cc_start: 0.8716 (m-30) cc_final: 0.8353 (m-30) REVERT: P 21 LYS cc_start: 0.6645 (mttm) cc_final: 0.6018 (mttp) outliers start: 39 outliers final: 27 residues processed: 198 average time/residue: 0.1182 time to fit residues: 31.8793 Evaluate side-chains 209 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 97 LYS 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 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain 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 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 6 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.096679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080667 restraints weight = 13483.205| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.28 r_work: 0.3081 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9882 Z= 0.154 Angle : 0.550 12.078 13320 Z= 0.289 Chirality : 0.050 0.141 1719 Planarity : 0.002 0.013 1674 Dihedral : 5.568 59.896 1449 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.19 % Allowed : 23.66 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR U 39 PHE 0.010 0.003 PHE R 94 HIS 0.002 0.000 HIS Z 50 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9882) covalent geometry : angle 0.55045 (13320) hydrogen bonds : bond 0.01557 ( 196) hydrogen bonds : angle 4.75596 ( 588) ********************** 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 207 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.370 Fit side-chains REVERT: K 38 LEU cc_start: 0.8818 (pp) cc_final: 0.8420 (pp) REVERT: K 61 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: L 43 LYS cc_start: 0.8713 (mttt) cc_final: 0.8449 (mtpp) REVERT: L 100 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4904 (tt) REVERT: M 28 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8196 (mt-10) REVERT: N 35 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: N 100 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5470 (tt) REVERT: Q 60 LYS cc_start: 0.7949 (tttp) cc_final: 0.7413 (ttmt) REVERT: R 100 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5949 (tt) REVERT: W 21 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7216 (mmtt) REVERT: Z 35 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: a 28 GLU cc_start: 0.8313 (tt0) cc_final: 0.7899 (tt0) REVERT: a 61 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8243 (mt-10) REVERT: b 35 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: b 95 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9039 (t) REVERT: b 98 ASP cc_start: 0.8577 (m-30) cc_final: 0.8126 (m-30) outliers start: 31 outliers final: 21 residues processed: 191 average time/residue: 0.1148 time to fit residues: 30.1723 Evaluate side-chains 204 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 VAL 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 81 THR 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 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 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 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 41 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.091981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076570 restraints weight = 13683.949| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.16 r_work: 0.2971 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.076 9882 Z= 0.497 Angle : 0.811 14.821 13320 Z= 0.429 Chirality : 0.059 0.203 1719 Planarity : 0.003 0.015 1674 Dihedral : 6.277 59.076 1449 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.70 % Allowed : 23.35 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.004 TYR Y 39 PHE 0.021 0.005 PHE R 94 HIS 0.004 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.01198 ( 9882) covalent geometry : angle 0.81060 (13320) hydrogen bonds : bond 0.02828 ( 196) hydrogen bonds : angle 5.39275 ( 588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2284.05 seconds wall clock time: 40 minutes 9.99 seconds (2409.99 seconds total)