Starting phenix.real_space_refine on Sun Dec 29 02:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cda_45465/12_2024/9cda_45465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cda_45465/12_2024/9cda_45465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cda_45465/12_2024/9cda_45465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cda_45465/12_2024/9cda_45465.map" model { file = "/net/cci-nas-00/data/ceres_data/9cda_45465/12_2024/9cda_45465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cda_45465/12_2024/9cda_45465.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6111 2.51 5 N 1737 2.21 5 O 2007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 2 Chain: "a" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 538 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "b" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 557 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Restraints were copied for chains: K, M, O, Q, S, U, W, Y, L, N, P, R, T, V, X, Z Time building chain proxies: 3.07, per 1000 atoms: 0.31 Number of scatterers: 9855 At special positions: 0 Unit cell: (110.922, 97.578, 63.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2007 8.00 N 1737 7.00 C 6111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'M' and resid 15 through 20 removed outlier: 6.375A pdb=" N VAL K 15 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA S 18 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA K 17 " --> pdb=" O ALA S 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU S 20 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA K 19 " --> pdb=" O GLU S 20 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL Q 15 " --> pdb=" O VAL W 16 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA W 18 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA Q 17 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU W 20 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA Q 19 " --> pdb=" O GLU W 20 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL U 15 " --> pdb=" O VAL a 16 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA a 18 " --> pdb=" O VAL U 15 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA U 17 " --> pdb=" O ALA a 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU a 20 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA U 19 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL Y 15 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA O 18 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA Y 17 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLU O 20 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA Y 19 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 24 through 34 removed outlier: 6.217A pdb=" N GLN K 24 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA M 27 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL K 26 " --> pdb=" O ALA M 27 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA M 29 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU K 28 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLY M 31 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ALA K 30 " --> pdb=" O GLY M 31 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR M 33 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS K 32 " --> pdb=" O THR M 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS S 32 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR K 33 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS S 34 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN Q 24 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA S 27 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Q 26 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA S 29 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU Q 28 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY S 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ALA Q 30 " --> pdb=" O GLY S 31 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR S 33 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS Q 32 " --> pdb=" O THR S 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS W 32 " --> pdb=" O GLY Q 31 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR Q 33 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS W 34 " --> pdb=" O THR Q 33 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN U 24 " --> pdb=" O GLY W 25 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA W 27 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL U 26 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA W 29 " --> pdb=" O VAL U 26 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU U 28 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLY W 31 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ALA U 30 " --> pdb=" O GLY W 31 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR W 33 " --> pdb=" O ALA U 30 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS U 32 " --> pdb=" O THR W 33 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS a 32 " --> pdb=" O GLY U 31 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR U 33 " --> pdb=" O LYS a 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS a 34 " --> pdb=" O THR U 33 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN Y 24 " --> pdb=" O GLY a 25 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA a 27 " --> pdb=" O GLN Y 24 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Y 26 " --> pdb=" O ALA a 27 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA a 29 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU Y 28 " --> pdb=" O ALA a 29 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY a 31 " --> pdb=" O GLU Y 28 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ALA Y 30 " --> pdb=" O GLY a 31 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR a 33 " --> pdb=" O ALA Y 30 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LYS Y 32 " --> pdb=" O THR a 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS O 32 " --> pdb=" O GLY Y 31 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR Y 33 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS O 34 " --> pdb=" O THR Y 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 38 through 40 removed outlier: 6.472A pdb=" N TYR K 39 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR Q 39 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR U 39 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR Y 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 46 through 55 removed outlier: 6.906A pdb=" N GLY M 47 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL K 52 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA M 53 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR K 54 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL M 55 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY K 47 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N HIS S 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL K 49 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL S 52 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY K 51 " --> pdb=" O VAL S 52 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N THR S 54 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA K 53 " --> pdb=" O THR S 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY S 47 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL Q 52 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA S 53 " --> pdb=" O VAL Q 52 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR Q 54 " --> pdb=" O ALA S 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL S 55 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY Q 47 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS W 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL Q 49 " --> pdb=" O HIS W 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL W 52 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY Q 51 " --> pdb=" O VAL W 52 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N THR W 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA Q 53 " --> pdb=" O THR W 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY W 47 " --> pdb=" O GLU U 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL U 52 " --> pdb=" O GLY W 51 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA W 53 " --> pdb=" O VAL U 52 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR U 54 " --> pdb=" O ALA W 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL W 55 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY U 47 " --> pdb=" O VAL a 48 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N HIS a 50 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL U 49 " --> pdb=" O HIS a 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL a 52 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY U 51 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N THR a 54 " --> pdb=" O GLY U 51 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ALA U 53 " --> pdb=" O THR a 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY a 47 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL Y 52 " --> pdb=" O GLY a 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA a 53 " --> pdb=" O VAL Y 52 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR Y 54 " --> pdb=" O ALA a 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL a 55 " --> pdb=" O THR Y 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY Y 47 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS O 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL Y 49 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL O 52 " --> pdb=" O VAL Y 49 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY Y 51 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N THR O 54 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA Y 53 " --> pdb=" O THR O 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 69 through 71 removed outlier: 6.498A pdb=" N ALA K 69 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA Q 69 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA U 69 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA Y 69 " --> pdb=" O VAL a 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 89 through 91 removed outlier: 6.244A pdb=" N ALA K 89 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA Q 89 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA U 89 " --> pdb=" O ALA W 90 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA Y 89 " --> pdb=" O ALA a 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 23 through 28 removed outlier: 7.022A pdb=" N GLN L 24 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY N 25 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N LYS L 23 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL T 26 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY L 25 " --> pdb=" O VAL T 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU T 28 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA L 27 " --> pdb=" O GLU T 28 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN R 24 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY T 25 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS R 23 " --> pdb=" O GLN X 24 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL X 26 " --> pdb=" O LYS R 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY R 25 " --> pdb=" O VAL X 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU X 28 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA R 27 " --> pdb=" O GLU X 28 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN V 24 " --> pdb=" O LYS X 23 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY X 25 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS V 23 " --> pdb=" O GLN b 24 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL b 26 " --> pdb=" O LYS V 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY V 25 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLU b 28 " --> pdb=" O GLY V 25 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA V 27 " --> pdb=" O GLU b 28 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN Z 24 " --> pdb=" O LYS b 23 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY b 25 " --> pdb=" O GLN Z 24 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LYS Z 23 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL P 26 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY Z 25 " --> pdb=" O VAL P 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU P 28 " --> pdb=" O GLY Z 25 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA Z 27 " --> pdb=" O GLU P 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 38 through 57 removed outlier: 6.866A pdb=" N TYR N 39 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL L 40 " --> pdb=" O TYR N 39 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY N 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER L 42 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS N 43 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR L 44 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS N 45 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU L 46 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY N 47 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL L 52 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA N 53 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR L 54 " --> pdb=" O ALA N 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL N 55 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA L 56 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU N 57 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N TYR L 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N SER T 42 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLY L 41 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N THR T 44 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LYS L 43 " --> pdb=" O THR T 44 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLU T 46 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS L 45 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL T 48 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY L 47 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS T 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL L 49 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL T 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY L 51 " --> pdb=" O VAL T 52 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR T 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA L 53 " --> pdb=" O THR T 54 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ALA T 56 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL L 55 " --> pdb=" O ALA T 56 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR T 39 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL R 40 " --> pdb=" O TYR T 39 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY T 41 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER R 42 " --> pdb=" O GLY T 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS T 43 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR R 44 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS T 45 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU R 46 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY T 47 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL R 52 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA T 53 " --> pdb=" O VAL R 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR R 54 " --> pdb=" O ALA T 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL T 55 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA R 56 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU T 57 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N TYR R 39 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N SER X 42 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLY R 41 " --> pdb=" O SER X 42 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N THR X 44 " --> pdb=" O GLY R 41 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N LYS R 43 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLU X 46 " --> pdb=" O LYS R 43 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS R 45 " --> pdb=" O GLU X 46 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL X 48 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY R 47 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS X 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL R 49 " --> pdb=" O HIS X 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY R 51 " --> pdb=" O VAL X 52 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N THR X 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA R 53 " --> pdb=" O THR X 54 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N ALA X 56 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL R 55 " --> pdb=" O ALA X 56 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR X 39 " --> pdb=" O LEU V 38 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL V 40 " --> pdb=" O TYR X 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY X 41 " --> pdb=" O VAL V 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER V 42 " --> pdb=" O GLY X 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS X 43 " --> pdb=" O SER V 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR V 44 " --> pdb=" O LYS X 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS X 45 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU V 46 " --> pdb=" O LYS X 45 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY X 47 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL V 52 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA X 53 " --> pdb=" O VAL V 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR V 54 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL X 55 " --> pdb=" O THR V 54 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA V 56 " --> pdb=" O VAL X 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU X 57 " --> pdb=" O ALA V 56 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N TYR V 39 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N SER b 42 " --> pdb=" O TYR V 39 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLY V 41 " --> pdb=" O SER b 42 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N THR b 44 " --> pdb=" O GLY V 41 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LYS V 43 " --> pdb=" O THR b 44 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLU b 46 " --> pdb=" O LYS V 43 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LYS V 45 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL b 48 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY V 47 " --> pdb=" O VAL b 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS b 50 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL V 49 " --> pdb=" O HIS b 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL b 52 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY V 51 " --> pdb=" O VAL b 52 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR b 54 " --> pdb=" O GLY V 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA V 53 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ALA b 56 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N VAL V 55 " --> pdb=" O ALA b 56 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR b 39 " --> pdb=" O LEU Z 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL Z 40 " --> pdb=" O TYR b 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY b 41 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER Z 42 " --> pdb=" O GLY b 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS b 43 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR Z 44 " --> pdb=" O LYS b 43 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS b 45 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU Z 46 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY b 47 " --> pdb=" O GLU Z 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL Z 52 " --> pdb=" O GLY b 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA b 53 " --> pdb=" O VAL Z 52 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR Z 54 " --> pdb=" O ALA b 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL b 55 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA Z 56 " --> pdb=" O VAL b 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU b 57 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N TYR Z 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N SER P 42 " --> pdb=" O TYR Z 39 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLY Z 41 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N THR P 44 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LYS Z 43 " --> pdb=" O THR P 44 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLU P 46 " --> pdb=" O LYS Z 43 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS Z 45 " --> pdb=" O GLU P 46 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL P 48 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY Z 47 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS P 50 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL Z 49 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL P 52 " --> pdb=" O VAL Z 49 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY Z 51 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR P 54 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA Z 53 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ALA P 56 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N VAL Z 55 " --> pdb=" O ALA P 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 60 through 66 removed outlier: 6.464A pdb=" N LYS L 60 " --> pdb=" O GLU N 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL N 63 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN L 62 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN N 65 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR L 64 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS R 60 " --> pdb=" O GLU T 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL T 63 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN R 62 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN T 65 " --> pdb=" O GLN R 62 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR R 64 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS V 60 " --> pdb=" O GLU X 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL X 63 " --> pdb=" O LYS V 60 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN V 62 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN X 65 " --> pdb=" O GLN V 62 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR V 64 " --> pdb=" O ASN X 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS Z 60 " --> pdb=" O GLU b 61 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL b 63 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN Z 62 " --> pdb=" O VAL b 63 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN b 65 " --> pdb=" O GLN Z 62 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR Z 64 " --> pdb=" O ASN b 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.587A pdb=" N VAL L 70 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL R 70 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL V 70 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL Z 70 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 74 through 82 removed outlier: 6.572A pdb=" N VAL L 74 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL T 77 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA L 76 " --> pdb=" O VAL T 77 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLN T 79 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA L 78 " --> pdb=" O GLN T 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR T 81 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS L 80 " --> pdb=" O THR T 81 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL R 74 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL X 77 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA R 76 " --> pdb=" O VAL X 77 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLN X 79 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA R 78 " --> pdb=" O GLN X 79 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR X 81 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS R 80 " --> pdb=" O THR X 81 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL V 74 " --> pdb=" O THR b 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL b 77 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA V 76 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLN b 79 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA V 78 " --> pdb=" O GLN b 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR b 81 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS V 80 " --> pdb=" O THR b 81 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL Z 74 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL P 77 " --> pdb=" O VAL Z 74 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA Z 76 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLN P 79 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA Z 78 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR P 81 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS Z 80 " --> pdb=" O THR P 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 88 through 96 removed outlier: 6.869A pdb=" N ALA N 89 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE L 94 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL N 95 " --> pdb=" O PHE L 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS L 96 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA L 89 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR T 92 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA L 91 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE T 94 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY L 93 " --> pdb=" O PHE T 94 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N LYS T 96 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N VAL L 95 " --> pdb=" O LYS T 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA T 89 " --> pdb=" O ILE R 88 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE R 94 " --> pdb=" O GLY T 93 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL T 95 " --> pdb=" O PHE R 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS R 96 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA R 89 " --> pdb=" O ALA X 90 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR X 92 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA R 91 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE X 94 " --> pdb=" O ALA R 91 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLY R 93 " --> pdb=" O PHE X 94 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N LYS X 96 " --> pdb=" O GLY R 93 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL R 95 " --> pdb=" O LYS X 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA X 89 " --> pdb=" O ILE V 88 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE V 94 " --> pdb=" O GLY X 93 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL X 95 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS V 96 " --> pdb=" O VAL X 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA V 89 " --> pdb=" O ALA b 90 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR b 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA V 91 " --> pdb=" O THR b 92 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE b 94 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY V 93 " --> pdb=" O PHE b 94 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N LYS b 96 " --> pdb=" O GLY V 93 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N VAL V 95 " --> pdb=" O LYS b 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA b 89 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE Z 94 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL b 95 " --> pdb=" O PHE Z 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS Z 96 " --> pdb=" O VAL b 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA Z 89 " --> pdb=" O ALA P 90 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR P 92 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA Z 91 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE P 94 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY Z 93 " --> pdb=" O PHE P 94 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N LYS P 96 " --> pdb=" O GLY Z 93 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL Z 95 " --> pdb=" O LYS P 96 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.69 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and resid 21 through 93) selection = (chain 'L' and resid 21 through 93) selection = (chain 'M' and resid 21 through 93) selection = (chain 'N' and resid 21 through 93) selection = (chain 'O' and resid 21 through 93) selection = (chain 'P' and resid 21 through 93) selection = (chain 'Q' and resid 21 through 93) selection = (chain 'R' and resid 21 through 93) selection = (chain 'S' and resid 21 through 93) selection = (chain 'T' and resid 21 through 93) selection = (chain 'U' and resid 21 through 93) selection = (chain 'V' and resid 21 through 93) selection = (chain 'W' and resid 21 through 93) selection = (chain 'X' and resid 21 through 93) selection = (chain 'Y' and resid 21 through 93) selection = (chain 'Z' and resid 21 through 93) selection = (chain 'a' and resid 21 through 93) selection = (chain 'b' and resid 21 through 93) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.840 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 9882 Z= 0.375 Angle : 0.586 6.224 13320 Z= 0.346 Chirality : 0.050 0.138 1719 Planarity : 0.002 0.012 1674 Dihedral : 18.156 70.318 3429 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.85 % Allowed : 18.52 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS a 50 PHE 0.010 0.003 PHE Z 94 TYR 0.012 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 1.033 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: 0.2889 time to fit residues: 94.9877 Evaluate side-chains 201 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain O residue 81 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN S 79 GLN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 HIS Y 24 GLN a 24 GLN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9882 Z= 0.217 Angle : 0.497 8.678 13320 Z= 0.271 Chirality : 0.051 0.180 1719 Planarity : 0.002 0.018 1674 Dihedral : 5.237 58.196 1453 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.91 % Allowed : 16.98 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.20), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Z 50 PHE 0.009 0.002 PHE V 94 TYR 0.010 0.002 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 1.160 Fit side-chains REVERT: K 38 LEU cc_start: 0.8789 (pp) cc_final: 0.8343 (pp) REVERT: L 43 LYS cc_start: 0.8685 (mttt) cc_final: 0.8476 (mtpp) REVERT: L 100 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4857 (tt) REVERT: N 45 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8245 (mttm) REVERT: R 83 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6191 (mt-10) REVERT: U 38 LEU cc_start: 0.8731 (pp) cc_final: 0.8434 (pp) REVERT: X 83 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6685 (mm-30) REVERT: X 97 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8272 (mttt) REVERT: Y 83 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6761 (mt-10) REVERT: a 79 GLN cc_start: 0.8492 (mt0) cc_final: 0.8230 (mt0) REVERT: O 20 GLU cc_start: 0.7390 (pm20) cc_final: 0.7116 (pt0) REVERT: P 45 LYS cc_start: 0.8641 (mttt) cc_final: 0.8278 (mttm) outliers start: 38 outliers final: 15 residues processed: 212 average time/residue: 0.2568 time to fit residues: 72.9668 Evaluate side-chains 189 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 100 LEU Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain b residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** M 24 GLN S 24 GLN a 50 HIS ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.056 9882 Z= 0.672 Angle : 0.721 12.516 13320 Z= 0.386 Chirality : 0.056 0.200 1719 Planarity : 0.003 0.017 1674 Dihedral : 5.979 58.298 1447 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.25 % Allowed : 17.18 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 50 PHE 0.016 0.004 PHE V 94 TYR 0.020 0.003 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 1.095 Fit side-chains REVERT: K 61 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: L 34 LYS cc_start: 0.7911 (mttt) cc_final: 0.7540 (mtpt) REVERT: L 43 LYS cc_start: 0.8747 (mttt) cc_final: 0.8469 (mtpp) REVERT: L 100 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4999 (tt) REVERT: M 61 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: X 83 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6973 (mm-30) REVERT: Y 23 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8100 (mmmt) REVERT: Z 83 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6690 (mt-10) REVERT: O 20 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: O 61 GLU cc_start: 0.8358 (mp0) cc_final: 0.7800 (mt-10) REVERT: P 21 LYS cc_start: 0.6853 (mttm) cc_final: 0.6537 (mttp) outliers start: 51 outliers final: 33 residues processed: 215 average time/residue: 0.2454 time to fit residues: 71.0285 Evaluate side-chains 210 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3026 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= 0.180 Angle : 0.493 9.713 13320 Z= 0.262 Chirality : 0.050 0.139 1719 Planarity : 0.002 0.013 1674 Dihedral : 5.296 59.139 1447 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.29 % Allowed : 20.47 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (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 HIS 0.002 0.000 HIS Z 50 PHE 0.009 0.002 PHE T 94 TYR 0.008 0.001 TYR U 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.133 Fit side-chains REVERT: K 38 LEU cc_start: 0.8778 (pp) cc_final: 0.8378 (pp) REVERT: L 43 LYS cc_start: 0.8702 (mttt) cc_final: 0.8461 (mtpp) REVERT: L 100 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4929 (tt) REVERT: U 38 LEU cc_start: 0.8770 (pp) cc_final: 0.8387 (pp) REVERT: Y 65 ASN cc_start: 0.8961 (t0) cc_final: 0.8673 (t0) REVERT: a 28 GLU cc_start: 0.7603 (tt0) cc_final: 0.7169 (tt0) REVERT: a 61 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7946 (mt-10) REVERT: b 95 VAL cc_start: 0.9420 (p) cc_final: 0.9053 (t) REVERT: O 20 GLU cc_start: 0.7765 (pm20) cc_final: 0.7408 (pt0) REVERT: O 21 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8296 (mptt) outliers start: 32 outliers final: 20 residues processed: 196 average time/residue: 0.2548 time to fit residues: 67.4451 Evaluate side-chains 190 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR 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 115 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9882 Z= 0.464 Angle : 0.611 12.690 13320 Z= 0.323 Chirality : 0.052 0.151 1719 Planarity : 0.002 0.014 1674 Dihedral : 5.647 57.464 1447 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.01 % Allowed : 20.68 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS a 50 PHE 0.014 0.004 PHE R 94 TYR 0.017 0.003 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 1.091 Fit side-chains REVERT: L 43 LYS cc_start: 0.8735 (mttt) cc_final: 0.8467 (mtpp) REVERT: L 100 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.5068 (tt) REVERT: R 100 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5829 (tt) REVERT: U 38 LEU cc_start: 0.8911 (pp) cc_final: 0.8577 (pp) REVERT: U 61 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: a 61 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7976 (mt-10) REVERT: b 98 ASP cc_start: 0.8609 (m-30) cc_final: 0.8358 (m-30) REVERT: P 21 LYS cc_start: 0.6897 (mttm) cc_final: 0.6578 (mttp) outliers start: 39 outliers final: 27 residues processed: 190 average time/residue: 0.2604 time to fit residues: 66.7684 Evaluate side-chains 198 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 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 34 LYS Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9882 Z= 0.263 Angle : 0.528 11.540 13320 Z= 0.279 Chirality : 0.050 0.140 1719 Planarity : 0.002 0.011 1674 Dihedral : 5.355 53.829 1447 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.01 % Allowed : 21.30 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS Z 50 PHE 0.011 0.003 PHE X 94 TYR 0.011 0.002 TYR U 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.992 Fit side-chains REVERT: K 38 LEU cc_start: 0.8820 (pp) cc_final: 0.8407 (pp) REVERT: L 43 LYS cc_start: 0.8716 (mttt) cc_final: 0.8473 (mtpp) REVERT: L 100 LEU cc_start: 0.5307 (OUTLIER) cc_final: 0.5030 (tt) REVERT: X 83 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6768 (mm-30) REVERT: Y 65 ASN cc_start: 0.9054 (t0) cc_final: 0.8804 (t0) REVERT: a 61 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7924 (mt-10) REVERT: b 95 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9050 (t) outliers start: 39 outliers final: 27 residues processed: 190 average time/residue: 0.2450 time to fit residues: 63.1780 Evaluate side-chains 191 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 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 33 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 0.0070 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 overall best weight: 2.3402 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9882 Z= 0.370 Angle : 0.582 12.686 13320 Z= 0.305 Chirality : 0.051 0.144 1719 Planarity : 0.002 0.015 1674 Dihedral : 5.472 54.847 1447 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.63 % Allowed : 20.27 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS a 50 PHE 0.013 0.003 PHE X 94 TYR 0.014 0.002 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.111 Fit side-chains REVERT: K 38 LEU cc_start: 0.8876 (pp) cc_final: 0.8430 (pp) REVERT: L 43 LYS cc_start: 0.8723 (mttt) cc_final: 0.8468 (mtpp) REVERT: L 100 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.4966 (tt) REVERT: R 100 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5852 (tt) REVERT: U 38 LEU cc_start: 0.8807 (pp) cc_final: 0.8576 (pp) REVERT: Y 65 ASN cc_start: 0.9154 (t0) cc_final: 0.8868 (t0) REVERT: Z 35 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: a 61 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8024 (mt-10) REVERT: b 98 ASP cc_start: 0.8591 (m-30) cc_final: 0.8339 (m-30) REVERT: P 21 LYS cc_start: 0.6914 (mttm) cc_final: 0.6514 (mttp) outliers start: 45 outliers final: 33 residues processed: 198 average time/residue: 0.2563 time to fit residues: 68.2912 Evaluate side-chains 207 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain R residue 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 U residue 87 SER Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR 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 55 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 9882 Z= 0.551 Angle : 0.683 13.313 13320 Z= 0.361 Chirality : 0.053 0.151 1719 Planarity : 0.003 0.024 1674 Dihedral : 5.785 58.884 1447 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.53 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS a 50 PHE 0.016 0.004 PHE V 94 TYR 0.018 0.003 TYR Y 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.077 Fit side-chains REVERT: L 43 LYS cc_start: 0.8704 (mttt) cc_final: 0.8451 (mtpp) REVERT: L 100 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.5019 (tt) REVERT: N 34 LYS cc_start: 0.8056 (mttt) cc_final: 0.7486 (mtpt) REVERT: N 43 LYS cc_start: 0.8796 (mttt) cc_final: 0.8588 (mttt) REVERT: N 100 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5281 (tt) REVERT: Q 60 LYS cc_start: 0.8031 (tttp) cc_final: 0.7547 (ttmt) REVERT: R 100 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5951 (tt) REVERT: Z 35 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: b 35 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: b 98 ASP cc_start: 0.8632 (m-30) cc_final: 0.8393 (m-30) REVERT: P 21 LYS cc_start: 0.6942 (mttm) cc_final: 0.6404 (mttp) outliers start: 44 outliers final: 35 residues processed: 209 average time/residue: 0.2554 time to fit residues: 71.3845 Evaluate side-chains 217 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain R residue 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 U residue 87 SER Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9882 Z= 0.285 Angle : 0.558 12.313 13320 Z= 0.293 Chirality : 0.050 0.142 1719 Planarity : 0.002 0.011 1674 Dihedral : 5.425 56.645 1447 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.01 % Allowed : 22.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS a 50 PHE 0.012 0.003 PHE X 94 TYR 0.011 0.002 TYR U 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 1.065 Fit side-chains REVERT: K 38 LEU cc_start: 0.8841 (pp) cc_final: 0.8414 (pp) REVERT: L 43 LYS cc_start: 0.8676 (mttt) cc_final: 0.8451 (mtpp) REVERT: L 100 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4818 (tt) REVERT: N 34 LYS cc_start: 0.8039 (mttt) cc_final: 0.7439 (mtpt) REVERT: N 60 LYS cc_start: 0.8849 (mttp) cc_final: 0.8630 (mttm) REVERT: N 100 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5330 (tt) REVERT: U 38 LEU cc_start: 0.8770 (pp) cc_final: 0.8526 (pp) REVERT: Z 35 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: a 61 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7968 (mt-10) REVERT: b 35 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: b 95 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9028 (t) REVERT: b 98 ASP cc_start: 0.8565 (m-30) cc_final: 0.8301 (m-30) outliers start: 39 outliers final: 30 residues processed: 202 average time/residue: 0.2537 time to fit residues: 68.6522 Evaluate side-chains 206 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 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 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 34 LYS 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 Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 23 LYS Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 9882 Z= 0.517 Angle : 0.665 13.685 13320 Z= 0.350 Chirality : 0.053 0.148 1719 Planarity : 0.002 0.012 1674 Dihedral : 5.736 59.556 1447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 4.12 % Allowed : 21.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.19), residues: 1404 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS a 50 PHE 0.016 0.004 PHE X 94 TYR 0.017 0.003 TYR Y 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.028 Fit side-chains REVERT: L 43 LYS cc_start: 0.8705 (mttt) cc_final: 0.8444 (mtpp) REVERT: L 100 LEU cc_start: 0.5313 (OUTLIER) cc_final: 0.4974 (tt) REVERT: N 100 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5428 (tt) REVERT: Q 60 LYS cc_start: 0.8045 (tttp) cc_final: 0.7537 (ttmt) REVERT: R 100 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.6021 (tt) REVERT: U 38 LEU cc_start: 0.8822 (pp) cc_final: 0.8567 (pp) REVERT: X 97 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8506 (mttt) REVERT: Z 35 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: a 61 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7952 (mt-10) REVERT: b 35 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: b 98 ASP cc_start: 0.8603 (m-30) cc_final: 0.8376 (m-30) REVERT: P 21 LYS cc_start: 0.6950 (mttm) cc_final: 0.6279 (mttp) outliers start: 40 outliers final: 33 residues processed: 196 average time/residue: 0.2586 time to fit residues: 68.7247 Evaluate side-chains 209 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain R residue 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 34 LYS Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 23 LYS Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9227 > 50: distance: 157 - 160: 19.350 distance: 160 - 161: 16.218 distance: 161 - 162: 9.729 distance: 161 - 164: 39.610 distance: 162 - 163: 9.200 distance: 162 - 165: 7.323 distance: 165 - 166: 36.363 distance: 166 - 167: 31.174 distance: 167 - 168: 16.673 distance: 167 - 169: 36.186 distance: 169 - 170: 19.613 distance: 170 - 171: 6.650 distance: 170 - 173: 13.407 distance: 171 - 172: 14.779 distance: 171 - 178: 7.878 distance: 173 - 174: 9.204 distance: 174 - 175: 15.691 distance: 175 - 176: 11.495 distance: 176 - 177: 5.934 distance: 178 - 179: 9.362 distance: 179 - 180: 7.220 distance: 179 - 182: 8.633 distance: 180 - 181: 35.050 distance: 180 - 185: 17.479 distance: 182 - 183: 6.145 distance: 182 - 184: 16.647 distance: 185 - 186: 22.530 distance: 186 - 187: 5.414 distance: 186 - 189: 20.211 distance: 187 - 194: 24.274 distance: 189 - 190: 26.691 distance: 190 - 191: 23.821 distance: 191 - 192: 33.453 distance: 192 - 193: 13.633 distance: 194 - 195: 18.608 distance: 195 - 196: 16.906 distance: 195 - 198: 14.019 distance: 196 - 203: 22.267 distance: 198 - 199: 10.493 distance: 199 - 200: 34.821 distance: 200 - 201: 24.122 distance: 200 - 202: 8.206 distance: 203 - 204: 22.636 distance: 204 - 205: 27.582 distance: 205 - 206: 39.215 distance: 205 - 207: 18.552 distance: 207 - 208: 11.688 distance: 208 - 209: 15.143 distance: 208 - 211: 28.081 distance: 209 - 210: 15.546 distance: 209 - 214: 11.912 distance: 211 - 212: 5.685 distance: 211 - 213: 18.390 distance: 214 - 215: 13.638 distance: 215 - 216: 8.679 distance: 215 - 218: 3.844 distance: 216 - 222: 8.729 distance: 218 - 219: 5.795 distance: 219 - 220: 5.468 distance: 219 - 221: 5.788 distance: 223 - 224: 6.449 distance: 224 - 225: 13.777 distance: 224 - 234: 6.415 distance: 227 - 229: 3.017