Starting phenix.real_space_refine on Tue Mar 3 13:00:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ssx_10307/03_2026/6ssx_10307.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ssx_10307/03_2026/6ssx_10307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ssx_10307/03_2026/6ssx_10307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ssx_10307/03_2026/6ssx_10307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ssx_10307/03_2026/6ssx_10307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ssx_10307/03_2026/6ssx_10307.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3050 2.51 5 N 860 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4900 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.67, per 1000 atoms: 0.14 Number of scatterers: 4900 At special positions: 0 Unit cell: (75.48, 117.623, 40.885, 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 990 8.00 N 860 7.00 C 3050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 480.6 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.132A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS A 21 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR C 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 21 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR D 22 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS C 21 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 57 removed outlier: 9.080A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N HIS B 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N THR B 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N ALA B 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N VAL A 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N VAL B 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N VAL C 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VAL C 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL D 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS D 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL C 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY C 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N THR D 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ALA D 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL C 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS E 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N THR E 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA D 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ALA E 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL D 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 93 Processing sheet with id=AA7, first strand: chain 'F' and resid 15 through 23 removed outlier: 6.129A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR G 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS F 21 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR I 22 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS H 21 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR J 22 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS I 21 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 57 removed outlier: 9.084A pdb=" N VAL F 37 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL G 40 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N SER G 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS G 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL F 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL G 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY F 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N THR G 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA F 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ALA G 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL F 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N VAL G 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL H 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ALA H 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL G 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N VAL H 37 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N VAL I 40 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.621A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS I 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL I 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N THR I 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ALA H 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ALA I 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N VAL H 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL I 37 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N VAL J 40 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS J 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL J 52 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY I 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N THR J 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA I 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N ALA J 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N VAL I 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB1, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 93 160 hydrogen bonds defined for protein. 480 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: 0.64 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 870 1.29 - 1.35: 770 1.35 - 1.41: 180 1.41 - 1.48: 831 1.48 - 1.54: 2259 Bond restraints: 4910 Sorted by residual: bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU H 38 " pdb=" CD1 LEU H 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU I 38 " pdb=" CD1 LEU I 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.55e+00 ... (remaining 4905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 5668 1.09 - 2.19: 720 2.19 - 3.28: 127 3.28 - 4.38: 70 4.38 - 5.47: 45 Bond angle restraints: 6630 Sorted by residual: angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" C THR I 44 " ideal model delta sigma weight residual 109.23 113.56 -4.33 1.55e+00 4.16e-01 7.79e+00 angle pdb=" N THR E 44 " pdb=" CA THR E 44 " pdb=" C THR E 44 " ideal model delta sigma weight residual 109.23 113.51 -4.28 1.55e+00 4.16e-01 7.63e+00 angle pdb=" N THR J 44 " pdb=" CA THR J 44 " pdb=" C THR J 44 " ideal model delta sigma weight residual 109.23 113.51 -4.28 1.55e+00 4.16e-01 7.61e+00 angle pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" C THR C 44 " ideal model delta sigma weight residual 109.23 113.50 -4.27 1.55e+00 4.16e-01 7.61e+00 angle pdb=" N THR G 44 " pdb=" CA THR G 44 " pdb=" C THR G 44 " ideal model delta sigma weight residual 109.23 113.50 -4.27 1.55e+00 4.16e-01 7.60e+00 ... (remaining 6625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 2500 16.71 - 33.41: 300 33.41 - 50.12: 20 50.12 - 66.82: 10 66.82 - 83.53: 10 Dihedral angle restraints: 2840 sinusoidal: 900 harmonic: 1940 Sorted by residual: dihedral pdb=" CA GLY G 73 " pdb=" C GLY G 73 " pdb=" N VAL G 74 " pdb=" CA VAL G 74 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA GLY B 73 " pdb=" C GLY B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual 180.00 148.99 31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY F 73 " pdb=" C GLY F 73 " pdb=" N VAL F 74 " pdb=" CA VAL F 74 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 428 0.040 - 0.079: 174 0.079 - 0.119: 200 0.119 - 0.159: 48 0.159 - 0.199: 20 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB THR H 44 " pdb=" CA THR H 44 " pdb=" OG1 THR H 44 " pdb=" CG2 THR H 44 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR E 44 " pdb=" CA THR E 44 " pdb=" OG1 THR E 44 " pdb=" CG2 THR E 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CB THR D 44 " pdb=" CA THR D 44 " pdb=" OG1 THR D 44 " pdb=" CG2 THR D 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 867 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 72 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C THR C 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR C 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 72 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C THR E 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR E 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 72 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C THR I 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR I 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY I 73 " 0.008 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2121 2.92 - 3.41: 4427 3.41 - 3.91: 8204 3.91 - 4.40: 9433 4.40 - 4.90: 17678 Nonbonded interactions: 41863 Sorted by model distance: nonbonded pdb=" OE1 GLN A 62 " pdb=" NE2 GLN B 62 " model vdw 2.424 3.120 nonbonded pdb=" OE1 GLN F 62 " pdb=" NE2 GLN G 62 " model vdw 2.454 3.120 nonbonded pdb=" N VAL F 74 " pdb=" O VAL G 74 " model vdw 2.479 3.120 nonbonded pdb=" N VAL A 74 " pdb=" O VAL B 74 " model vdw 2.480 3.120 nonbonded pdb=" N LYS A 58 " pdb=" O GLU B 57 " model vdw 2.483 3.120 ... (remaining 41858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain '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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.730 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.008 0.053 4910 Z= 0.376 Angle : 0.938 5.474 6630 Z= 0.553 Chirality : 0.069 0.199 870 Planarity : 0.004 0.014 830 Dihedral : 14.938 83.526 1620 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 4.26 % Allowed : 6.38 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.005 TYR E 39 PHE 0.007 0.002 PHE D 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00816 ( 4910) covalent geometry : angle 0.93752 ( 6630) hydrogen bonds : bond 0.08154 ( 160) hydrogen bonds : angle 4.71940 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.105 Fit side-chains REVERT: B 80 LYS cc_start: 0.8097 (mttp) cc_final: 0.7744 (mtpt) REVERT: E 80 LYS cc_start: 0.8592 (mttp) cc_final: 0.8309 (mtpp) REVERT: F 65 ASN cc_start: 0.9013 (m-40) cc_final: 0.8789 (m-40) REVERT: J 80 LYS cc_start: 0.8250 (mttp) cc_final: 0.7879 (mtmt) outliers start: 20 outliers final: 4 residues processed: 67 average time/residue: 0.6358 time to fit residues: 44.0805 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.146150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.126946 restraints weight = 5388.454| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.31 r_work: 0.3884 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4910 Z= 0.146 Angle : 0.587 6.459 6630 Z= 0.337 Chirality : 0.053 0.132 870 Planarity : 0.002 0.017 830 Dihedral : 7.659 41.576 724 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.47 % Allowed : 10.21 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR B 39 PHE 0.003 0.001 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4910) covalent geometry : angle 0.58723 ( 6630) hydrogen bonds : bond 0.01654 ( 160) hydrogen bonds : angle 3.50574 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.223 Fit side-chains REVERT: B 80 LYS cc_start: 0.8210 (mttp) cc_final: 0.7687 (mtpt) REVERT: D 80 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8246 (mtpm) REVERT: E 80 LYS cc_start: 0.8620 (mttp) cc_final: 0.8090 (mtpp) REVERT: J 58 LYS cc_start: 0.7676 (ttmt) cc_final: 0.6816 (tptm) REVERT: J 83 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7897 (mt-10) outliers start: 21 outliers final: 8 residues processed: 60 average time/residue: 0.5674 time to fit residues: 35.4218 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.135139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.116523 restraints weight = 5599.422| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.20 r_work: 0.3750 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4910 Z= 0.360 Angle : 0.702 6.128 6630 Z= 0.407 Chirality : 0.057 0.144 870 Planarity : 0.003 0.011 830 Dihedral : 8.059 42.569 723 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 5.11 % Allowed : 10.64 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.005 TYR I 39 PHE 0.008 0.002 PHE D 94 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00774 ( 4910) covalent geometry : angle 0.70244 ( 6630) hydrogen bonds : bond 0.02057 ( 160) hydrogen bonds : angle 4.09396 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.174 Fit side-chains REVERT: B 80 LYS cc_start: 0.8321 (mttp) cc_final: 0.7774 (mtpt) REVERT: C 24 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7176 (mm-40) REVERT: D 24 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7008 (mt0) REVERT: E 80 LYS cc_start: 0.8752 (mttp) cc_final: 0.8099 (mtpp) REVERT: F 65 ASN cc_start: 0.9110 (m-40) cc_final: 0.8891 (m-40) REVERT: H 60 LYS cc_start: 0.7822 (mttt) cc_final: 0.7306 (mtpp) REVERT: J 46 GLU cc_start: 0.8216 (tp30) cc_final: 0.7971 (tm-30) REVERT: J 58 LYS cc_start: 0.7837 (ttmt) cc_final: 0.6858 (tptm) outliers start: 24 outliers final: 15 residues processed: 70 average time/residue: 0.6599 time to fit residues: 47.7572 Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.143360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.124819 restraints weight = 5385.281| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.26 r_work: 0.3845 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4910 Z= 0.143 Angle : 0.572 6.736 6630 Z= 0.328 Chirality : 0.053 0.132 870 Planarity : 0.002 0.010 830 Dihedral : 7.024 41.669 722 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.11 % Allowed : 12.34 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR B 39 PHE 0.003 0.001 PHE C 94 HIS 0.001 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4910) covalent geometry : angle 0.57238 ( 6630) hydrogen bonds : bond 0.01397 ( 160) hydrogen bonds : angle 3.58368 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.157 Fit side-chains REVERT: B 23 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7505 (mtpp) REVERT: B 80 LYS cc_start: 0.8194 (mttp) cc_final: 0.7725 (mtpt) REVERT: C 83 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7857 (mt-10) REVERT: G 58 LYS cc_start: 0.7543 (tttt) cc_final: 0.7154 (tttm) REVERT: I 83 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8073 (mt-10) REVERT: J 46 GLU cc_start: 0.8045 (tp30) cc_final: 0.7706 (tm-30) REVERT: J 58 LYS cc_start: 0.7675 (ttmt) cc_final: 0.6737 (tptm) outliers start: 24 outliers final: 14 residues processed: 61 average time/residue: 0.6056 time to fit residues: 38.3395 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 63 optimal weight: 10.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.135806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.117570 restraints weight = 5689.038| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.14 r_work: 0.3752 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4910 Z= 0.325 Angle : 0.671 6.078 6630 Z= 0.389 Chirality : 0.056 0.143 870 Planarity : 0.003 0.010 830 Dihedral : 7.580 41.264 722 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 4.89 % Allowed : 13.62 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.004 TYR I 39 PHE 0.008 0.001 PHE D 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 4910) covalent geometry : angle 0.67132 ( 6630) hydrogen bonds : bond 0.01909 ( 160) hydrogen bonds : angle 4.09808 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.181 Fit side-chains REVERT: B 80 LYS cc_start: 0.8223 (mttp) cc_final: 0.7760 (mtpt) REVERT: C 60 LYS cc_start: 0.7560 (mttt) cc_final: 0.7311 (mtmt) REVERT: E 80 LYS cc_start: 0.8723 (mttp) cc_final: 0.8073 (mtpp) REVERT: F 65 ASN cc_start: 0.9075 (m-40) cc_final: 0.8863 (m-40) REVERT: G 20 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: G 58 LYS cc_start: 0.7617 (tttt) cc_final: 0.7242 (tttm) REVERT: H 60 LYS cc_start: 0.7771 (mttt) cc_final: 0.7280 (mtpp) REVERT: J 46 GLU cc_start: 0.8086 (tp30) cc_final: 0.7780 (tp30) REVERT: J 58 LYS cc_start: 0.7779 (ttmt) cc_final: 0.6788 (tptm) outliers start: 23 outliers final: 16 residues processed: 65 average time/residue: 0.6363 time to fit residues: 42.8642 Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.140889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.122659 restraints weight = 5825.184| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.25 r_work: 0.3853 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4910 Z= 0.126 Angle : 0.565 7.213 6630 Z= 0.324 Chirality : 0.053 0.130 870 Planarity : 0.002 0.010 830 Dihedral : 6.802 40.938 722 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.89 % Allowed : 14.04 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.003 0.001 PHE C 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4910) covalent geometry : angle 0.56490 ( 6630) hydrogen bonds : bond 0.01312 ( 160) hydrogen bonds : angle 3.58544 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.176 Fit side-chains REVERT: B 23 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7496 (mtpp) REVERT: B 80 LYS cc_start: 0.8126 (mttp) cc_final: 0.7444 (mtpt) REVERT: G 58 LYS cc_start: 0.7617 (tttt) cc_final: 0.7258 (tttm) REVERT: H 60 LYS cc_start: 0.7648 (mttt) cc_final: 0.7194 (mtpp) REVERT: J 46 GLU cc_start: 0.7936 (tp30) cc_final: 0.7598 (tp30) REVERT: J 58 LYS cc_start: 0.7761 (ttmt) cc_final: 0.6781 (tptm) outliers start: 23 outliers final: 18 residues processed: 60 average time/residue: 0.6059 time to fit residues: 37.6414 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.134743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.115905 restraints weight = 5635.286| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.24 r_work: 0.3736 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4910 Z= 0.317 Angle : 0.666 6.997 6630 Z= 0.386 Chirality : 0.055 0.143 870 Planarity : 0.003 0.010 830 Dihedral : 7.456 40.753 722 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 4.68 % Allowed : 15.96 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.004 TYR I 39 PHE 0.008 0.001 PHE D 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 4910) covalent geometry : angle 0.66599 ( 6630) hydrogen bonds : bond 0.01878 ( 160) hydrogen bonds : angle 4.07950 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.134 Fit side-chains REVERT: B 80 LYS cc_start: 0.8138 (mttp) cc_final: 0.7616 (mtpp) REVERT: C 60 LYS cc_start: 0.7597 (mttt) cc_final: 0.7332 (mtpt) REVERT: E 80 LYS cc_start: 0.8697 (mttp) cc_final: 0.8184 (mtpp) REVERT: G 58 LYS cc_start: 0.7686 (tttt) cc_final: 0.7337 (tttm) REVERT: H 60 LYS cc_start: 0.7799 (mttt) cc_final: 0.7331 (mtpp) REVERT: J 46 GLU cc_start: 0.8032 (tp30) cc_final: 0.7740 (tp30) REVERT: J 58 LYS cc_start: 0.7770 (ttmt) cc_final: 0.6826 (tptm) outliers start: 22 outliers final: 19 residues processed: 65 average time/residue: 0.6393 time to fit residues: 42.9191 Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.141111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.123295 restraints weight = 5797.737| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.30 r_work: 0.3858 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4910 Z= 0.126 Angle : 0.572 6.913 6630 Z= 0.328 Chirality : 0.053 0.130 870 Planarity : 0.002 0.010 830 Dihedral : 6.716 40.619 722 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.47 % Allowed : 15.53 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.003 0.001 PHE C 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4910) covalent geometry : angle 0.57211 ( 6630) hydrogen bonds : bond 0.01307 ( 160) hydrogen bonds : angle 3.61437 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.174 Fit side-chains REVERT: B 80 LYS cc_start: 0.8043 (mttp) cc_final: 0.7547 (mtpp) REVERT: C 23 LYS cc_start: 0.7626 (mtpt) cc_final: 0.7318 (mtpp) REVERT: G 58 LYS cc_start: 0.7644 (tttt) cc_final: 0.7269 (tttm) REVERT: H 60 LYS cc_start: 0.7650 (mttt) cc_final: 0.7190 (mtpp) REVERT: J 46 GLU cc_start: 0.7921 (tp30) cc_final: 0.7546 (tp30) REVERT: J 58 LYS cc_start: 0.7724 (ttmt) cc_final: 0.6752 (tptm) outliers start: 21 outliers final: 14 residues processed: 57 average time/residue: 0.5708 time to fit residues: 33.7813 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.135288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.117245 restraints weight = 5926.780| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.27 r_work: 0.3768 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4910 Z= 0.244 Angle : 0.621 5.876 6630 Z= 0.359 Chirality : 0.054 0.138 870 Planarity : 0.002 0.011 830 Dihedral : 7.108 39.643 722 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 3.83 % Allowed : 16.81 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR I 39 PHE 0.006 0.001 PHE D 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 4910) covalent geometry : angle 0.62143 ( 6630) hydrogen bonds : bond 0.01674 ( 160) hydrogen bonds : angle 3.84724 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.186 Fit side-chains REVERT: B 80 LYS cc_start: 0.8002 (mttp) cc_final: 0.7522 (mtpp) REVERT: C 60 LYS cc_start: 0.7467 (mttt) cc_final: 0.7209 (mtpt) REVERT: C 83 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7927 (mt-10) REVERT: E 80 LYS cc_start: 0.8625 (mttp) cc_final: 0.8088 (mtpp) REVERT: H 60 LYS cc_start: 0.7711 (mttt) cc_final: 0.7266 (mtpp) REVERT: J 46 GLU cc_start: 0.7939 (tp30) cc_final: 0.7648 (tp30) REVERT: J 58 LYS cc_start: 0.7733 (ttmt) cc_final: 0.6737 (tptp) outliers start: 18 outliers final: 16 residues processed: 63 average time/residue: 0.6595 time to fit residues: 42.9599 Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.132826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115281 restraints weight = 5836.916| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.21 r_work: 0.3756 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4910 Z= 0.255 Angle : 0.649 6.371 6630 Z= 0.373 Chirality : 0.055 0.143 870 Planarity : 0.002 0.010 830 Dihedral : 7.303 40.775 722 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.62 % Allowed : 17.02 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR I 39 PHE 0.006 0.001 PHE D 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 4910) covalent geometry : angle 0.64887 ( 6630) hydrogen bonds : bond 0.01658 ( 160) hydrogen bonds : angle 3.93319 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.165 Fit side-chains REVERT: B 80 LYS cc_start: 0.7914 (mttp) cc_final: 0.7536 (mtpp) REVERT: C 60 LYS cc_start: 0.7487 (mttt) cc_final: 0.7190 (mtpt) REVERT: C 83 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7956 (mt-10) REVERT: E 80 LYS cc_start: 0.8537 (mttp) cc_final: 0.8094 (mtpp) REVERT: G 57 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6959 (mp0) REVERT: H 60 LYS cc_start: 0.7726 (mttt) cc_final: 0.7245 (mtpp) REVERT: J 46 GLU cc_start: 0.8023 (tp30) cc_final: 0.7649 (tp30) REVERT: J 58 LYS cc_start: 0.7754 (ttmt) cc_final: 0.6764 (tptp) outliers start: 17 outliers final: 16 residues processed: 62 average time/residue: 0.6557 time to fit residues: 42.0127 Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.134240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.116914 restraints weight = 5820.951| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.24 r_work: 0.3797 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4910 Z= 0.195 Angle : 0.629 7.489 6630 Z= 0.360 Chirality : 0.054 0.137 870 Planarity : 0.002 0.009 830 Dihedral : 7.018 41.002 722 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.26 % Allowed : 16.17 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.005 0.001 PHE D 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4910) covalent geometry : angle 0.62867 ( 6630) hydrogen bonds : bond 0.01470 ( 160) hydrogen bonds : angle 3.75226 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.47 seconds wall clock time: 28 minutes 8.91 seconds (1688.91 seconds total)