Starting phenix.real_space_refine on Wed Oct 9 23:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck3_45639/10_2024/9ck3_45639.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck3_45639/10_2024/9ck3_45639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck3_45639/10_2024/9ck3_45639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck3_45639/10_2024/9ck3_45639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck3_45639/10_2024/9ck3_45639.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck3_45639/10_2024/9ck3_45639.cif" } resolution = 2.04 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= 0.002 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 3612 2.51 5 N 996 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 5748 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 479 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 2.59, per 1000 atoms: 0.45 Number of scatterers: 5748 At special positions: 0 Unit cell: (102.582, 108.42, 48.372, 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 1140 8.00 N 996 7.00 C 3612 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: 1.42 Conformation dependent library (CDL) restraints added in 766.3 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 72.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 21 removed outlier: 6.504A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA E 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLU F 20 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA E 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 57 removed outlier: 6.512A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY B 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS B 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS B 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLY B 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY C 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS C 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER B 42 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LYS C 45 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 44 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY C 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N GLU B 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL C 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLU C 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY D 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS D 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER C 42 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LYS D 45 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLY D 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLU C 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL D 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N GLY D 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS C 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ALA D 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL D 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU D 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL E 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS D 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY E 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY F 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS F 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER E 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS F 45 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR E 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLY F 47 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLU E 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL F 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLY F 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU F 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA E 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.494A pdb=" N LYS E 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL D 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN E 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASN D 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 82 removed outlier: 9.023A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 10.243A pdb=" N THR B 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N VAL B 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 73 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA B 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR A 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA B 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N LYS B 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N GLN A 79 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL B 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N THR A 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N THR C 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N VAL C 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY B 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALA C 76 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR B 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA C 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N LYS C 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLN B 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N VAL C 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA C 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N THR D 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N VAL C 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N VAL D 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA D 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N LYS D 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N GLN C 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL D 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N THR C 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY D 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA E 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN D 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS E 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR D 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL E 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N ALA E 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N THR F 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N VAL E 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N VAL F 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY E 73 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA F 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR E 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA F 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N VAL E 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N LYS F 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N GLN E 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL F 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N THR E 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 92 removed outlier: 9.042A pdb=" N GLY A 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N ALA B 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N GLY B 86 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N ALA C 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ALA C 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA B 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLY C 86 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N ALA D 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA D 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER E 87 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE D 88 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA E 89 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLY E 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N ALA F 89 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE E 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ALA F 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA E 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.458A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL E 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 21 removed outlier: 6.504A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU H 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA G 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA K 17 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU L 20 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA K 19 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 37 through 57 removed outlier: 6.511A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY H 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL G 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS H 43 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER G 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LYS H 45 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR G 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY H 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLU G 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL H 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N VAL G 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N GLY H 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS G 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ALA H 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL G 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL H 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR G 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLU H 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA G 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU H 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLY I 41 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL H 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LYS I 43 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER H 42 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LYS I 45 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR H 44 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY I 47 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N GLU H 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL I 49 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N VAL H 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N GLY I 51 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL I 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLU I 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA H 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS J 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER I 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LYS J 45 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR I 44 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLY J 47 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N GLU I 46 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL J 49 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N VAL I 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N GLY J 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS I 50 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ALA J 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL I 52 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL J 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU J 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA I 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL J 48 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL K 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS J 50 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY K 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU K 38 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLY L 41 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL K 40 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS L 43 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER K 42 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS L 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR K 44 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLY L 47 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLU K 46 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL L 49 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N VAL K 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N GLY L 51 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU L 57 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA K 56 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 60 through 66 removed outlier: 6.494A pdb=" N LYS K 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL J 63 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN K 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASN J 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR K 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 69 through 82 removed outlier: 9.022A pdb=" N ALA G 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 10.243A pdb=" N THR H 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N VAL G 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N VAL H 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY G 73 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA H 76 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N LYS H 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLN G 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL H 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N THR G 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N ALA H 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N THR I 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N VAL H 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N VAL I 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY H 73 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA I 76 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR H 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA I 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N VAL H 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N LYS I 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N GLN H 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N VAL I 82 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N THR H 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N ALA I 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 10.243A pdb=" N THR J 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N VAL I 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL J 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY I 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA J 76 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N LYS J 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N GLN I 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL J 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N THR I 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL K 70 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL J 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR K 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY J 73 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL J 77 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA K 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN J 79 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS K 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR J 81 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL K 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA K 69 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 10.243A pdb=" N THR L 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N VAL K 71 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL L 74 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY K 73 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA L 76 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR K 75 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA L 78 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N VAL K 77 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N LYS L 80 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N GLN K 79 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL L 82 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N THR K 81 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 86 through 92 removed outlier: 9.042A pdb=" N GLY G 86 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N ALA H 89 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ALA H 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA G 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N ALA I 89 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA I 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA H 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLY I 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N ALA J 89 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA J 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER K 87 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE J 88 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA K 89 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLY K 86 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N ALA L 89 " --> pdb=" O GLY K 86 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE K 88 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA L 91 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA K 90 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 95 through 96 removed outlier: 6.459A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL H 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL I 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL K 95 " --> pdb=" O LYS L 96 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 996 1.29 - 1.35: 888 1.35 - 1.42: 204 1.42 - 1.48: 949 1.48 - 1.55: 2723 Bond restraints: 5760 Sorted by residual: bond pdb=" CB THR F 72 " pdb=" CG2 THR F 72 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.20e-01 bond pdb=" CB THR H 72 " pdb=" CG2 THR H 72 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.09e-01 bond pdb=" CB THR I 72 " pdb=" CG2 THR I 72 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.03e-01 bond pdb=" CB THR B 72 " pdb=" CG2 THR B 72 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.01e-01 bond pdb=" CB THR C 72 " pdb=" CG2 THR C 72 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.91e-01 ... (remaining 5755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 6865 0.87 - 1.73: 719 1.73 - 2.60: 120 2.60 - 3.47: 36 3.47 - 4.33: 36 Bond angle restraints: 7776 Sorted by residual: angle pdb=" C VAL J 49 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " ideal model delta sigma weight residual 121.85 117.52 4.33 1.77e+00 3.19e-01 5.99e+00 angle pdb=" C VAL L 49 " pdb=" N HIS L 50 " pdb=" CA HIS L 50 " ideal model delta sigma weight residual 121.85 117.52 4.33 1.77e+00 3.19e-01 5.99e+00 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.85 117.52 4.33 1.77e+00 3.19e-01 5.97e+00 angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 121.85 117.53 4.32 1.77e+00 3.19e-01 5.97e+00 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 121.85 117.54 4.31 1.77e+00 3.19e-01 5.94e+00 ... (remaining 7771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2952 17.67 - 35.34: 252 35.34 - 53.01: 84 53.01 - 70.68: 60 70.68 - 88.35: 24 Dihedral angle restraints: 3372 sinusoidal: 1104 harmonic: 2268 Sorted by residual: dihedral pdb=" CA LYS I 97 " pdb=" CB LYS I 97 " pdb=" CG LYS I 97 " pdb=" CD LYS I 97 " ideal model delta sinusoidal sigma weight residual -180.00 -120.00 -60.00 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS D 97 " pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " pdb=" CD LYS D 97 " ideal model delta sinusoidal sigma weight residual -180.00 -120.00 -60.00 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS B 97 " pdb=" CB LYS B 97 " pdb=" CG LYS B 97 " pdb=" CD LYS B 97 " ideal model delta sinusoidal sigma weight residual -180.00 -120.00 -60.00 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 518 0.025 - 0.050: 239 0.050 - 0.075: 83 0.075 - 0.100: 74 0.100 - 0.125: 130 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB THR H 72 " pdb=" CA THR H 72 " pdb=" OG1 THR H 72 " pdb=" CG2 THR H 72 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CB THR I 72 " pdb=" CA THR I 72 " pdb=" OG1 THR I 72 " pdb=" CG2 THR I 72 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1041 not shown) Planarity restraints: 948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " 0.009 2.00e-02 2.50e+03 7.94e-03 9.46e-01 pdb=" CG HIS F 50 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 50 " -0.009 2.00e-02 2.50e+03 7.94e-03 9.46e-01 pdb=" CG HIS K 50 " 0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS K 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS K 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS K 50 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.009 2.00e-02 2.50e+03 7.93e-03 9.44e-01 pdb=" CG HIS E 50 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.003 2.00e-02 2.50e+03 ... (remaining 945 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 3163 3.01 - 3.48: 5297 3.48 - 3.95: 8366 3.95 - 4.43: 10269 4.43 - 4.90: 20213 Nonbonded interactions: 47308 Sorted by model distance: nonbonded pdb=" O GLY K 36 " pdb=" N GLY L 36 " model vdw 2.532 3.120 nonbonded pdb=" O GLY C 36 " pdb=" N GLY D 36 " model vdw 2.533 3.120 nonbonded pdb=" O GLY E 36 " pdb=" N GLY F 36 " model vdw 2.533 3.120 nonbonded pdb=" O GLY A 36 " pdb=" N GLY B 36 " model vdw 2.533 3.120 nonbonded pdb=" O GLY G 36 " pdb=" N GLY H 36 " model vdw 2.533 3.120 ... (remaining 47303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.220 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 : 0.004 0.024 5760 Z= 0.282 Angle : 0.643 4.333 7776 Z= 0.371 Chirality : 0.053 0.125 1044 Planarity : 0.002 0.008 948 Dihedral : 19.964 88.354 1932 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.08 % Allowed : 20.83 % Favored : 77.08 % 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: -0.15 (0.32), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.10 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS K 50 PHE 0.012 0.003 PHE L 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 0.656 Fit side-chains REVERT: B 60 LYS cc_start: 0.8480 (mttm) cc_final: 0.8270 (mtpm) REVERT: C 43 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7976 (mttt) REVERT: C 62 GLN cc_start: 0.8256 (mt0) cc_final: 0.8031 (tt0) REVERT: D 80 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8887 (tttp) REVERT: I 62 GLN cc_start: 0.8317 (mt0) cc_final: 0.8054 (tt0) outliers start: 12 outliers final: 5 residues processed: 189 average time/residue: 1.7625 time to fit residues: 342.8473 Evaluate side-chains 166 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain L residue 80 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 7.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 79 GLN E 79 GLN F 79 GLN C 79 GLN D 79 GLN G 79 GLN H 79 GLN K 79 GLN L 79 GLN I 79 GLN J 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 5760 Z= 0.578 Angle : 0.731 5.233 7776 Z= 0.418 Chirality : 0.069 0.168 1044 Planarity : 0.003 0.011 948 Dihedral : 7.236 50.893 852 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.51 % Allowed : 18.06 % Favored : 77.43 % 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: -0.42 (0.30), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.31 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS B 50 PHE 0.016 0.004 PHE B 94 TYR 0.013 0.004 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 0.689 Fit side-chains REVERT: E 39 TYR cc_start: 0.8256 (t80) cc_final: 0.7950 (t80) REVERT: C 43 LYS cc_start: 0.8276 (mtpt) cc_final: 0.8047 (mttt) REVERT: C 62 GLN cc_start: 0.8253 (mt0) cc_final: 0.8005 (tt0) outliers start: 26 outliers final: 18 residues processed: 181 average time/residue: 1.6230 time to fit residues: 303.0066 Evaluate side-chains 194 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain J residue 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5760 Z= 0.134 Angle : 0.475 6.046 7776 Z= 0.264 Chirality : 0.054 0.137 1044 Planarity : 0.001 0.007 948 Dihedral : 4.258 11.170 828 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.17 % Allowed : 21.88 % Favored : 73.96 % 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: -0.34 (0.30), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.25 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS I 50 PHE 0.009 0.002 PHE C 94 TYR 0.017 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 0.655 Fit side-chains REVERT: B 60 LYS cc_start: 0.8490 (mtpm) cc_final: 0.8242 (mttp) REVERT: B 62 GLN cc_start: 0.8296 (mt0) cc_final: 0.8085 (tt0) REVERT: E 80 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8728 (tttm) outliers start: 24 outliers final: 21 residues processed: 184 average time/residue: 1.6420 time to fit residues: 311.2999 Evaluate side-chains 198 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 0.0040 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5760 Z= 0.304 Angle : 0.576 6.255 7776 Z= 0.325 Chirality : 0.059 0.156 1044 Planarity : 0.002 0.009 948 Dihedral : 4.834 12.159 828 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.34 % Allowed : 22.22 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.30), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.013 0.003 PHE B 94 TYR 0.013 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 0.663 Fit side-chains REVERT: E 80 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8787 (tttm) outliers start: 25 outliers final: 22 residues processed: 181 average time/residue: 1.6673 time to fit residues: 311.1750 Evaluate side-chains 201 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5760 Z= 0.196 Angle : 0.522 6.688 7776 Z= 0.288 Chirality : 0.055 0.146 1044 Planarity : 0.002 0.007 948 Dihedral : 4.492 11.220 828 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.17 % Allowed : 23.61 % Favored : 72.22 % 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: -0.37 (0.30), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.27 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 50 PHE 0.011 0.003 PHE C 94 TYR 0.016 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 0.664 Fit side-chains REVERT: B 62 GLN cc_start: 0.8322 (mt0) cc_final: 0.8112 (tt0) REVERT: E 80 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8764 (tttm) REVERT: I 60 LYS cc_start: 0.8442 (mtpm) cc_final: 0.8171 (mttm) outliers start: 24 outliers final: 23 residues processed: 178 average time/residue: 1.6372 time to fit residues: 300.5461 Evaluate side-chains 196 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5760 Z= 0.424 Angle : 0.652 7.027 7776 Z= 0.368 Chirality : 0.063 0.164 1044 Planarity : 0.002 0.010 948 Dihedral : 5.086 12.760 828 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.69 % Allowed : 22.22 % Favored : 73.09 % 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: -0.48 (0.29), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS H 50 PHE 0.015 0.003 PHE C 94 TYR 0.015 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 0.652 Fit side-chains REVERT: E 80 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8804 (tttm) REVERT: I 60 LYS cc_start: 0.8475 (mtpm) cc_final: 0.8245 (mttp) outliers start: 27 outliers final: 24 residues processed: 179 average time/residue: 1.7031 time to fit residues: 314.3424 Evaluate side-chains 198 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5760 Z= 0.266 Angle : 0.565 6.985 7776 Z= 0.314 Chirality : 0.058 0.151 1044 Planarity : 0.002 0.008 948 Dihedral : 4.755 11.544 828 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.17 % Allowed : 23.61 % Favored : 72.22 % 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: -0.45 (0.30), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.33 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.012 0.003 PHE C 94 TYR 0.017 0.002 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 0.709 Fit side-chains REVERT: B 62 GLN cc_start: 0.8332 (mt0) cc_final: 0.8131 (tt0) REVERT: E 80 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8789 (tttm) outliers start: 24 outliers final: 22 residues processed: 179 average time/residue: 1.7131 time to fit residues: 316.1389 Evaluate side-chains 199 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 5760 Z= 0.476 Angle : 0.682 7.171 7776 Z= 0.387 Chirality : 0.066 0.165 1044 Planarity : 0.003 0.010 948 Dihedral : 5.186 13.038 828 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.86 % Allowed : 22.40 % Favored : 72.74 % 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: -0.54 (0.29), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.40 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS H 50 PHE 0.014 0.004 PHE H 94 TYR 0.018 0.003 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 0.651 Fit side-chains REVERT: A 45 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8248 (mtpt) REVERT: E 80 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8910 (tttm) outliers start: 28 outliers final: 25 residues processed: 175 average time/residue: 1.6890 time to fit residues: 304.6263 Evaluate side-chains 198 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5760 Z= 0.228 Angle : 0.547 7.189 7776 Z= 0.304 Chirality : 0.057 0.149 1044 Planarity : 0.002 0.008 948 Dihedral : 4.689 11.227 828 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.34 % Allowed : 23.26 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.34 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.011 0.003 PHE C 94 TYR 0.018 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.642 Fit side-chains REVERT: B 62 GLN cc_start: 0.8341 (mt0) cc_final: 0.8132 (tt0) REVERT: E 80 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8768 (tttm) outliers start: 25 outliers final: 23 residues processed: 180 average time/residue: 1.6468 time to fit residues: 305.4162 Evaluate side-chains 200 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5760 Z= 0.438 Angle : 0.664 7.111 7776 Z= 0.375 Chirality : 0.064 0.164 1044 Planarity : 0.002 0.010 948 Dihedral : 5.118 12.643 828 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.51 % Allowed : 22.74 % Favored : 72.74 % 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: -0.55 (0.29), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.41 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 50 PHE 0.014 0.003 PHE H 94 TYR 0.017 0.003 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 0.674 Fit side-chains outliers start: 26 outliers final: 24 residues processed: 177 average time/residue: 1.6401 time to fit residues: 299.4932 Evaluate side-chains 195 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.145793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.111888 restraints weight = 5018.632| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.55 r_work: 0.3697 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5760 Z= 0.289 Angle : 0.583 7.231 7776 Z= 0.324 Chirality : 0.059 0.153 1044 Planarity : 0.002 0.009 948 Dihedral : 4.853 11.889 828 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.34 % Allowed : 23.26 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 50 PHE 0.012 0.003 PHE C 94 TYR 0.017 0.003 TYR H 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4445.67 seconds wall clock time: 79 minutes 12.21 seconds (4752.21 seconds total)