Starting phenix.real_space_refine on Fri Feb 6 07:11:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sie_54927/02_2026/9sie_54927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sie_54927/02_2026/9sie_54927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sie_54927/02_2026/9sie_54927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sie_54927/02_2026/9sie_54927.map" model { file = "/net/cci-nas-00/data/ceres_data/9sie_54927/02_2026/9sie_54927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sie_54927/02_2026/9sie_54927.cif" } resolution = 2.7 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= 0.001 sd= 0.007 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 14773 2.51 5 N 3706 2.21 5 O 4845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23324 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Restraints were copied for chains: D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S Time building chain proxies: 1.80, per 1000 atoms: 0.08 Number of scatterers: 23324 At special positions: 0 Unit cell: (111.84, 110.4, 207.36, 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 4845 8.00 N 3706 7.00 C 14773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 967.4 milliseconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 34 sheets defined 24.6% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'C' and resid 4 through 48 removed outlier: 3.936A pdb=" N ILE C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 48 removed outlier: 3.936A pdb=" N ILE D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 48 removed outlier: 3.936A pdb=" N ILE E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE G 8 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE H 8 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG H 47 " --> pdb=" O LEU H 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE I 8 " --> pdb=" O LEU I 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG I 47 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG J 47 " --> pdb=" O LEU J 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG K 47 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL M 46 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG M 47 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 48 removed outlier: 3.936A pdb=" N ILE N 8 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG N 47 " --> pdb=" O LEU N 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE O 8 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG O 47 " --> pdb=" O LEU O 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL P 46 " --> pdb=" O GLY P 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG P 47 " --> pdb=" O LEU P 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL Q 46 " --> pdb=" O GLY Q 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG Q 47 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL R 46 " --> pdb=" O GLY R 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 48 removed outlier: 3.935A pdb=" N ILE S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL S 46 " --> pdb=" O GLY S 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL C 69 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU C 61 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR C 75 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER C 55 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 77 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS C 53 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AA3, first strand: chain 'D' and resid 112 through 115 removed outlier: 7.513A pdb=" N VAL D 69 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU D 61 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR D 75 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER D 55 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA D 77 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS D 53 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'E' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL E 69 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU E 61 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR E 75 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER E 55 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA E 77 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS E 53 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'F' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL F 69 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU F 61 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR F 75 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER F 55 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA F 77 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS F 53 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 106 through 108 Processing sheet with id=AA9, first strand: chain 'G' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL G 69 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU G 61 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR G 75 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER G 55 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA G 77 " --> pdb=" O LYS G 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS G 53 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'H' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL H 69 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU H 61 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR H 75 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER H 55 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA H 77 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS H 53 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 106 through 108 Processing sheet with id=AB4, first strand: chain 'I' and resid 112 through 115 removed outlier: 7.511A pdb=" N VAL I 69 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU I 61 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR I 75 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER I 55 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA I 77 " --> pdb=" O LYS I 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS I 53 " --> pdb=" O ALA I 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'J' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL J 69 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU J 61 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR J 75 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER J 55 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA J 77 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS J 53 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 106 through 108 Processing sheet with id=AB8, first strand: chain 'K' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL K 69 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU K 61 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR K 75 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER K 55 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA K 77 " --> pdb=" O LYS K 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS K 53 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 106 through 108 Processing sheet with id=AC1, first strand: chain 'L' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL L 69 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU L 61 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR L 75 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER L 55 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA L 77 " --> pdb=" O LYS L 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS L 53 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AC3, first strand: chain 'M' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL M 69 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU M 61 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR M 75 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER M 55 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA M 77 " --> pdb=" O LYS M 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS M 53 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 106 through 108 Processing sheet with id=AC5, first strand: chain 'N' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL N 69 " --> pdb=" O GLU N 61 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU N 61 " --> pdb=" O VAL N 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR N 75 " --> pdb=" O SER N 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER N 55 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA N 77 " --> pdb=" O LYS N 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS N 53 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 106 through 108 Processing sheet with id=AC7, first strand: chain 'O' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL O 69 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU O 61 " --> pdb=" O VAL O 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR O 75 " --> pdb=" O SER O 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER O 55 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA O 77 " --> pdb=" O LYS O 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS O 53 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'P' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL P 69 " --> pdb=" O GLU P 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU P 61 " --> pdb=" O VAL P 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR P 75 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER P 55 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA P 77 " --> pdb=" O LYS P 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS P 53 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'Q' and resid 112 through 115 removed outlier: 7.512A pdb=" N VAL Q 69 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU Q 61 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR Q 75 " --> pdb=" O SER Q 55 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER Q 55 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA Q 77 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS Q 53 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 112 through 115 removed outlier: 7.511A pdb=" N VAL R 69 " --> pdb=" O GLU R 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU R 61 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR R 75 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER R 55 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA R 77 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS R 53 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 106 through 108 Processing sheet with id=AD6, first strand: chain 'S' and resid 112 through 115 removed outlier: 7.511A pdb=" N VAL S 69 " --> pdb=" O GLU S 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU S 61 " --> pdb=" O VAL S 69 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR S 75 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER S 55 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA S 77 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS S 53 " --> pdb=" O ALA S 77 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 106 through 108 1105 hydrogen bonds defined for protein. 3162 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: 3.76 Time building geometry restraints manager: 2.85 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: 4148 1.29 - 1.35: 3602 1.35 - 1.42: 1736 1.42 - 1.48: 3823 1.48 - 1.54: 10372 Bond restraints: 23681 Sorted by residual: bond pdb=" CB VAL L 114 " pdb=" CG2 VAL L 114 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CB VAL K 114 " pdb=" CG2 VAL K 114 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CB VAL O 114 " pdb=" CG2 VAL O 114 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB VAL P 114 " pdb=" CG2 VAL P 114 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB VAL I 114 " pdb=" CG2 VAL I 114 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 23676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 32092 2.32 - 4.65: 294 4.65 - 6.97: 67 6.97 - 9.29: 0 9.29 - 11.61: 17 Bond angle restraints: 32470 Sorted by residual: angle pdb=" CA LEU L 135 " pdb=" CB LEU L 135 " pdb=" CG LEU L 135 " ideal model delta sigma weight residual 116.30 104.69 11.61 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU E 135 " pdb=" CB LEU E 135 " pdb=" CG LEU E 135 " ideal model delta sigma weight residual 116.30 104.70 11.60 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU J 135 " pdb=" CB LEU J 135 " pdb=" CG LEU J 135 " ideal model delta sigma weight residual 116.30 104.72 11.58 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU N 135 " pdb=" CB LEU N 135 " pdb=" CG LEU N 135 " ideal model delta sigma weight residual 116.30 104.73 11.57 3.50e+00 8.16e-02 1.09e+01 angle pdb=" CA LEU D 135 " pdb=" CB LEU D 135 " pdb=" CG LEU D 135 " ideal model delta sigma weight residual 116.30 104.73 11.57 3.50e+00 8.16e-02 1.09e+01 ... (remaining 32465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 12784 16.06 - 32.11: 1035 32.11 - 48.17: 87 48.17 - 64.22: 34 64.22 - 80.28: 17 Dihedral angle restraints: 13957 sinusoidal: 5015 harmonic: 8942 Sorted by residual: dihedral pdb=" CA GLN G 132 " pdb=" C GLN G 132 " pdb=" N GLY G 133 " pdb=" CA GLY G 133 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLN C 132 " pdb=" C GLN C 132 " pdb=" N GLY C 133 " pdb=" CA GLY C 133 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLN O 132 " pdb=" C GLN O 132 " pdb=" N GLY O 133 " pdb=" CA GLY O 133 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 13954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2810 0.041 - 0.082: 825 0.082 - 0.123: 508 0.123 - 0.164: 5 0.164 - 0.205: 17 Chirality restraints: 4165 Sorted by residual: chirality pdb=" CB ILE L 138 " pdb=" CA ILE L 138 " pdb=" CG1 ILE L 138 " pdb=" CG2 ILE L 138 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE I 138 " pdb=" CA ILE I 138 " pdb=" CG1 ILE I 138 " pdb=" CG2 ILE I 138 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE N 138 " pdb=" CA ILE N 138 " pdb=" CG1 ILE N 138 " pdb=" CG2 ILE N 138 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4162 not shown) Planarity restraints: 4131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 159 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.76e+00 pdb=" N PRO G 160 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 160 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 160 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 159 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO H 160 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 160 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 160 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 159 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO F 160 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 160 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 160 " -0.027 5.00e-02 4.00e+02 ... (remaining 4128 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 285 2.63 - 3.20: 23856 3.20 - 3.76: 32556 3.76 - 4.33: 45651 4.33 - 4.90: 73827 Nonbonded interactions: 176175 Sorted by model distance: nonbonded pdb=" OG1 THR E 2 " pdb=" OG1 THR I 6 " model vdw 2.061 3.040 nonbonded pdb=" OG1 THR C 6 " pdb=" OG1 THR R 2 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR G 6 " pdb=" OG1 THR H 2 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR F 2 " pdb=" OG1 THR O 6 " model vdw 2.320 3.040 nonbonded pdb=" O VAL C 15 " pdb=" OG SER C 18 " model vdw 2.341 3.040 ... (remaining 176170 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: 0.05 Found NCS groups: ncs_group { reference = 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 8.360 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: 0.860 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 17.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 23681 Z= 0.273 Angle : 0.750 11.615 32470 Z= 0.419 Chirality : 0.049 0.205 4165 Planarity : 0.007 0.048 4131 Dihedral : 11.834 80.279 8177 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.82 (0.15), residues: 3077 helix: -1.81 (0.16), residues: 663 sheet: -0.01 (0.17), residues: 1071 loop : -1.83 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 47 TYR 0.008 0.001 TYR E 40 PHE 0.009 0.002 PHE G 74 TRP 0.002 0.001 TRP J 112 HIS 0.004 0.002 HIS H 107 Details of bonding type rmsd covalent geometry : bond 0.00605 (23681) covalent geometry : angle 0.75046 (32470) hydrogen bonds : bond 0.16547 ( 1105) hydrogen bonds : angle 8.85255 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASN cc_start: 0.8522 (m110) cc_final: 0.8205 (m-40) REVERT: D 33 GLU cc_start: 0.9539 (tp30) cc_final: 0.8518 (tp30) REVERT: D 37 GLU cc_start: 0.8747 (pt0) cc_final: 0.8231 (pm20) REVERT: D 157 GLU cc_start: 0.8664 (tt0) cc_final: 0.8190 (tt0) REVERT: D 180 ASN cc_start: 0.7230 (m110) cc_final: 0.6865 (m-40) REVERT: E 33 GLU cc_start: 0.9386 (tp30) cc_final: 0.8946 (tp30) REVERT: F 33 GLU cc_start: 0.9485 (tp30) cc_final: 0.9000 (tp30) REVERT: G 33 GLU cc_start: 0.9521 (tp30) cc_final: 0.9041 (tp30) REVERT: G 99 ASP cc_start: 0.8257 (m-30) cc_final: 0.8026 (m-30) REVERT: H 33 GLU cc_start: 0.9495 (tp30) cc_final: 0.8923 (tp30) REVERT: I 5 GLU cc_start: 0.9157 (pp20) cc_final: 0.8884 (pp20) REVERT: I 9 ILE cc_start: 0.8751 (mp) cc_final: 0.8507 (mp) REVERT: I 33 GLU cc_start: 0.9440 (tp30) cc_final: 0.9209 (tp30) REVERT: I 45 GLU cc_start: 0.8813 (mp0) cc_final: 0.8461 (mp0) REVERT: J 33 GLU cc_start: 0.9547 (tp30) cc_final: 0.9008 (tp30) REVERT: J 157 GLU cc_start: 0.8736 (tt0) cc_final: 0.8237 (tt0) REVERT: J 180 ASN cc_start: 0.7805 (m110) cc_final: 0.7550 (m-40) REVERT: L 33 GLU cc_start: 0.9374 (tp30) cc_final: 0.8791 (tp30) REVERT: L 99 ASP cc_start: 0.8327 (m-30) cc_final: 0.8078 (m-30) REVERT: M 33 GLU cc_start: 0.9480 (tp30) cc_final: 0.9070 (tp30) REVERT: N 33 GLU cc_start: 0.9465 (tp30) cc_final: 0.9056 (tp30) REVERT: O 33 GLU cc_start: 0.9398 (tp30) cc_final: 0.8869 (tp30) REVERT: O 45 GLU cc_start: 0.8771 (mp0) cc_final: 0.8526 (mp0) REVERT: P 36 LYS cc_start: 0.9470 (ttpp) cc_final: 0.9246 (tttp) REVERT: P 99 ASP cc_start: 0.8276 (m-30) cc_final: 0.7954 (m-30) REVERT: Q 33 GLU cc_start: 0.9534 (tp30) cc_final: 0.8993 (tp30) REVERT: R 33 GLU cc_start: 0.9381 (tp30) cc_final: 0.9080 (tm-30) REVERT: S 33 GLU cc_start: 0.9495 (tp30) cc_final: 0.8884 (tm-30) REVERT: S 119 LYS cc_start: 0.7434 (mmmm) cc_final: 0.6806 (mptt) REVERT: S 157 GLU cc_start: 0.8538 (tt0) cc_final: 0.8201 (tt0) REVERT: S 180 ASN cc_start: 0.8327 (m110) cc_final: 0.7794 (m110) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.8161 time to fit residues: 411.0425 Evaluate side-chains 340 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 GLN J 169 GLN M 169 GLN N 169 GLN R 180 ASN S 151 ASN S 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.062276 restraints weight = 56767.015| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.10 r_work: 0.2726 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23681 Z= 0.210 Angle : 0.652 11.017 32470 Z= 0.344 Chirality : 0.049 0.201 4165 Planarity : 0.005 0.055 4131 Dihedral : 4.617 23.631 3264 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.05 % Allowed : 13.12 % Favored : 84.83 % 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: -0.49 (0.15), residues: 3077 helix: 1.74 (0.17), residues: 680 sheet: 0.81 (0.17), residues: 935 loop : -2.25 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 34 TYR 0.008 0.001 TYR R 40 PHE 0.019 0.002 PHE D 20 TRP 0.005 0.001 TRP D 112 HIS 0.004 0.002 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00473 (23681) covalent geometry : angle 0.65173 (32470) hydrogen bonds : bond 0.09102 ( 1105) hydrogen bonds : angle 5.22784 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 431 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8306 (pp20) REVERT: C 37 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8954 (pt0) REVERT: C 45 GLU cc_start: 0.9006 (mp0) cc_final: 0.8688 (mp0) REVERT: D 33 GLU cc_start: 0.9532 (tp30) cc_final: 0.8938 (tm-30) REVERT: D 34 ARG cc_start: 0.8925 (tpp-160) cc_final: 0.8074 (mmp80) REVERT: D 37 GLU cc_start: 0.9294 (pt0) cc_final: 0.8957 (pt0) REVERT: D 119 LYS cc_start: 0.7874 (mmmm) cc_final: 0.6968 (mptt) REVERT: D 180 ASN cc_start: 0.7563 (m110) cc_final: 0.7091 (m110) REVERT: H 33 GLU cc_start: 0.9543 (tp30) cc_final: 0.9303 (tm-30) REVERT: I 45 GLU cc_start: 0.8916 (mp0) cc_final: 0.8555 (mp0) REVERT: J 33 GLU cc_start: 0.9572 (tp30) cc_final: 0.9254 (mm-30) REVERT: J 34 ARG cc_start: 0.9128 (mmp80) cc_final: 0.8687 (mmp80) REVERT: J 37 GLU cc_start: 0.9247 (pt0) cc_final: 0.8968 (pm20) REVERT: J 157 GLU cc_start: 0.9001 (tt0) cc_final: 0.8617 (tt0) REVERT: J 159 LYS cc_start: 0.9108 (mttt) cc_final: 0.8831 (mttm) REVERT: J 180 ASN cc_start: 0.8186 (m110) cc_final: 0.7630 (m110) REVERT: K 33 GLU cc_start: 0.9491 (tp30) cc_final: 0.8910 (pp20) REVERT: K 34 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6972 (mmm160) REVERT: K 37 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8948 (pt0) REVERT: K 45 GLU cc_start: 0.8751 (mp0) cc_final: 0.8550 (mp0) REVERT: M 33 GLU cc_start: 0.9556 (tp30) cc_final: 0.9323 (tm-30) REVERT: O 45 GLU cc_start: 0.8946 (mp0) cc_final: 0.8631 (mp0) REVERT: P 33 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9137 (tm-30) REVERT: Q 180 ASN cc_start: 0.8589 (m110) cc_final: 0.8188 (m-40) REVERT: R 33 GLU cc_start: 0.9462 (tp30) cc_final: 0.8955 (pp20) REVERT: R 45 GLU cc_start: 0.8896 (mp0) cc_final: 0.8568 (mp0) REVERT: R 87 LEU cc_start: 0.8918 (mp) cc_final: 0.8708 (mp) REVERT: S 180 ASN cc_start: 0.8532 (m110) cc_final: 0.8032 (m110) outliers start: 53 outliers final: 22 residues processed: 451 average time/residue: 0.7089 time to fit residues: 358.4631 Evaluate side-chains 373 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 270 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.062731 restraints weight = 56682.393| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.11 r_work: 0.2741 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23681 Z= 0.177 Angle : 0.614 10.616 32470 Z= 0.322 Chirality : 0.048 0.140 4165 Planarity : 0.005 0.049 4131 Dihedral : 4.267 21.997 3264 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.26 % Allowed : 13.62 % Favored : 81.11 % 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: -0.10 (0.15), residues: 3077 helix: 2.90 (0.17), residues: 680 sheet: 0.09 (0.17), residues: 1071 loop : -1.88 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 34 TYR 0.008 0.001 TYR N 40 PHE 0.009 0.001 PHE P 20 TRP 0.004 0.001 TRP D 112 HIS 0.002 0.001 HIS N 107 Details of bonding type rmsd covalent geometry : bond 0.00393 (23681) covalent geometry : angle 0.61447 (32470) hydrogen bonds : bond 0.08192 ( 1105) hydrogen bonds : angle 4.82610 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 396 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8136 (pp20) REVERT: C 34 ARG cc_start: 0.7471 (tmt170) cc_final: 0.7048 (mmm160) REVERT: C 37 GLU cc_start: 0.9234 (pp20) cc_final: 0.8787 (pt0) REVERT: D 33 GLU cc_start: 0.9560 (tp30) cc_final: 0.8921 (tp30) REVERT: D 34 ARG cc_start: 0.9088 (tpp-160) cc_final: 0.8725 (mmp80) REVERT: D 119 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7137 (mptt) REVERT: D 180 ASN cc_start: 0.7587 (m110) cc_final: 0.7173 (m110) REVERT: I 33 GLU cc_start: 0.9638 (tp30) cc_final: 0.9188 (tm-30) REVERT: I 37 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9148 (pt0) REVERT: I 45 GLU cc_start: 0.8771 (mp0) cc_final: 0.8224 (tp30) REVERT: I 48 SER cc_start: 0.9409 (m) cc_final: 0.9142 (m) REVERT: J 33 GLU cc_start: 0.9611 (tp30) cc_final: 0.9382 (mm-30) REVERT: J 87 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9075 (tt) REVERT: J 119 LYS cc_start: 0.7876 (mmmm) cc_final: 0.7076 (mptt) REVERT: J 180 ASN cc_start: 0.8202 (m110) cc_final: 0.7724 (m110) REVERT: K 33 GLU cc_start: 0.9476 (tp30) cc_final: 0.8894 (pp20) REVERT: K 37 GLU cc_start: 0.9146 (pp20) cc_final: 0.8906 (pt0) REVERT: M 33 GLU cc_start: 0.9641 (tp30) cc_final: 0.9064 (tp30) REVERT: N 37 GLU cc_start: 0.9303 (pt0) cc_final: 0.9085 (pt0) REVERT: O 33 GLU cc_start: 0.9519 (tp30) cc_final: 0.9122 (tp30) REVERT: O 45 GLU cc_start: 0.8821 (mp0) cc_final: 0.8167 (tp30) REVERT: O 48 SER cc_start: 0.9381 (m) cc_final: 0.9097 (m) REVERT: P 37 GLU cc_start: 0.9196 (pt0) cc_final: 0.8824 (pt0) REVERT: Q 34 ARG cc_start: 0.9364 (mmp80) cc_final: 0.8905 (mmp80) REVERT: Q 37 GLU cc_start: 0.9325 (pt0) cc_final: 0.8878 (pt0) REVERT: Q 180 ASN cc_start: 0.8579 (m110) cc_final: 0.8086 (m110) REVERT: R 33 GLU cc_start: 0.9488 (tp30) cc_final: 0.8920 (tm-30) REVERT: R 87 LEU cc_start: 0.8982 (mp) cc_final: 0.8745 (mp) REVERT: S 119 LYS cc_start: 0.7840 (mmmm) cc_final: 0.6874 (mptt) REVERT: S 180 ASN cc_start: 0.8582 (m110) cc_final: 0.8084 (m110) outliers start: 136 outliers final: 74 residues processed: 479 average time/residue: 0.7037 time to fit residues: 381.6950 Evaluate side-chains 428 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 352 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 169 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 165 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 55 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.078728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.063466 restraints weight = 56869.960| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.14 r_work: 0.2758 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23681 Z= 0.161 Angle : 0.615 13.516 32470 Z= 0.316 Chirality : 0.047 0.135 4165 Planarity : 0.004 0.050 4131 Dihedral : 4.040 21.560 3264 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.80 % Allowed : 15.17 % Favored : 80.03 % 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: 0.27 (0.15), residues: 3077 helix: 3.36 (0.18), residues: 680 sheet: 0.97 (0.17), residues: 952 loop : -2.12 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 34 TYR 0.009 0.001 TYR R 40 PHE 0.010 0.001 PHE M 20 TRP 0.003 0.000 TRP D 112 HIS 0.002 0.001 HIS N 107 Details of bonding type rmsd covalent geometry : bond 0.00350 (23681) covalent geometry : angle 0.61451 (32470) hydrogen bonds : bond 0.07644 ( 1105) hydrogen bonds : angle 4.57623 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 396 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.9237 (pp20) cc_final: 0.8896 (pt0) REVERT: D 33 GLU cc_start: 0.9600 (tp30) cc_final: 0.8933 (tp30) REVERT: D 34 ARG cc_start: 0.9112 (tpp-160) cc_final: 0.8679 (mmp80) REVERT: D 37 GLU cc_start: 0.9291 (pt0) cc_final: 0.8930 (pt0) REVERT: D 119 LYS cc_start: 0.8024 (mmmm) cc_final: 0.7174 (mptt) REVERT: D 180 ASN cc_start: 0.7480 (m110) cc_final: 0.7086 (m110) REVERT: I 45 GLU cc_start: 0.8720 (mp0) cc_final: 0.8337 (mp0) REVERT: J 33 GLU cc_start: 0.9630 (tp30) cc_final: 0.9354 (mm-30) REVERT: J 37 GLU cc_start: 0.9312 (pt0) cc_final: 0.8952 (pt0) REVERT: J 119 LYS cc_start: 0.7922 (mmmm) cc_final: 0.7098 (mptt) REVERT: J 157 GLU cc_start: 0.9000 (tt0) cc_final: 0.8695 (tt0) REVERT: J 180 ASN cc_start: 0.8149 (m110) cc_final: 0.7694 (m110) REVERT: K 37 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8789 (pt0) REVERT: K 45 GLU cc_start: 0.8676 (mp0) cc_final: 0.8307 (mp0) REVERT: N 33 GLU cc_start: 0.9490 (tm-30) cc_final: 0.9141 (tm-30) REVERT: N 37 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8914 (pt0) REVERT: O 45 GLU cc_start: 0.8726 (mp0) cc_final: 0.8273 (tp30) REVERT: O 48 SER cc_start: 0.9321 (m) cc_final: 0.9060 (m) REVERT: P 33 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9087 (tp30) REVERT: P 37 GLU cc_start: 0.9159 (pt0) cc_final: 0.8931 (pt0) REVERT: Q 180 ASN cc_start: 0.8531 (m110) cc_final: 0.8048 (m110) REVERT: R 33 GLU cc_start: 0.9473 (tp30) cc_final: 0.8883 (tm-30) REVERT: R 34 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5485 (mmm-85) REVERT: R 87 LEU cc_start: 0.8999 (mp) cc_final: 0.8755 (mp) REVERT: S 119 LYS cc_start: 0.7849 (mmmm) cc_final: 0.6880 (mptt) REVERT: S 180 ASN cc_start: 0.8526 (m110) cc_final: 0.8056 (m110) outliers start: 124 outliers final: 79 residues processed: 472 average time/residue: 0.7023 time to fit residues: 375.6928 Evaluate side-chains 450 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 368 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 169 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 181 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 214 optimal weight: 0.0040 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 299 optimal weight: 4.9990 chunk 305 optimal weight: 20.0000 overall best weight: 4.6000 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.076046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.061156 restraints weight = 57488.310| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.10 r_work: 0.2707 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23681 Z= 0.214 Angle : 0.666 13.109 32470 Z= 0.343 Chirality : 0.048 0.135 4165 Planarity : 0.005 0.052 4131 Dihedral : 4.231 21.651 3264 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.15 % Allowed : 17.18 % Favored : 77.67 % 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: 0.27 (0.15), residues: 3077 helix: 3.75 (0.17), residues: 646 sheet: 0.24 (0.17), residues: 1071 loop : -1.76 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.007 0.001 TYR N 40 PHE 0.010 0.002 PHE G 20 TRP 0.003 0.001 TRP J 112 HIS 0.002 0.001 HIS N 107 Details of bonding type rmsd covalent geometry : bond 0.00499 (23681) covalent geometry : angle 0.66601 (32470) hydrogen bonds : bond 0.08227 ( 1105) hydrogen bonds : angle 4.73566 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 360 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6190 (mmt180) REVERT: C 37 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: D 33 GLU cc_start: 0.9596 (tp30) cc_final: 0.8901 (tp30) REVERT: D 34 ARG cc_start: 0.9197 (tpp-160) cc_final: 0.8776 (mmp80) REVERT: D 37 GLU cc_start: 0.9309 (pt0) cc_final: 0.8936 (pt0) REVERT: D 119 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7220 (mptt) REVERT: D 180 ASN cc_start: 0.7479 (m110) cc_final: 0.7086 (m110) REVERT: G 37 GLU cc_start: 0.9244 (tt0) cc_final: 0.8715 (pt0) REVERT: I 45 GLU cc_start: 0.8675 (mp0) cc_final: 0.8292 (tp30) REVERT: J 33 GLU cc_start: 0.9629 (tp30) cc_final: 0.9367 (mm-30) REVERT: J 37 GLU cc_start: 0.9342 (pt0) cc_final: 0.9113 (pt0) REVERT: J 119 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7142 (mptt) REVERT: J 157 GLU cc_start: 0.8993 (tt0) cc_final: 0.8759 (tt0) REVERT: J 180 ASN cc_start: 0.8143 (m110) cc_final: 0.7665 (m110) REVERT: K 33 GLU cc_start: 0.9522 (tp30) cc_final: 0.8884 (tm-30) REVERT: K 37 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8892 (pt0) REVERT: K 45 GLU cc_start: 0.8690 (mp0) cc_final: 0.8339 (mp0) REVERT: N 37 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9064 (pt0) REVERT: O 5 GLU cc_start: 0.8994 (pm20) cc_final: 0.8782 (pm20) REVERT: O 45 GLU cc_start: 0.8693 (mp0) cc_final: 0.8296 (tp30) REVERT: O 48 SER cc_start: 0.9454 (m) cc_final: 0.9193 (m) REVERT: P 33 GLU cc_start: 0.9499 (tm-30) cc_final: 0.9052 (tp30) REVERT: P 37 GLU cc_start: 0.9203 (pt0) cc_final: 0.8825 (pt0) REVERT: Q 180 ASN cc_start: 0.8555 (m110) cc_final: 0.8065 (m110) REVERT: R 33 GLU cc_start: 0.9552 (tp30) cc_final: 0.8868 (tm-30) REVERT: R 34 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.5423 (mmm-85) REVERT: R 45 GLU cc_start: 0.8843 (mp0) cc_final: 0.8433 (mp0) REVERT: S 33 GLU cc_start: 0.9603 (tp30) cc_final: 0.9314 (mm-30) REVERT: S 119 LYS cc_start: 0.8022 (mmmm) cc_final: 0.6954 (mptt) REVERT: S 180 ASN cc_start: 0.8449 (m110) cc_final: 0.7945 (m110) outliers start: 133 outliers final: 87 residues processed: 454 average time/residue: 0.7187 time to fit residues: 369.1895 Evaluate side-chains 431 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 339 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 169 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 169 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 72 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 156 optimal weight: 0.0040 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.066072 restraints weight = 56270.977| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.22 r_work: 0.2808 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23681 Z= 0.134 Angle : 0.609 15.208 32470 Z= 0.307 Chirality : 0.046 0.132 4165 Planarity : 0.004 0.052 4131 Dihedral : 3.769 18.491 3264 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.53 % Allowed : 19.39 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.15), residues: 3077 helix: 4.12 (0.17), residues: 646 sheet: 0.29 (0.17), residues: 1054 loop : -1.62 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 34 TYR 0.014 0.001 TYR R 40 PHE 0.013 0.001 PHE E 30 TRP 0.004 0.000 TRP R 112 HIS 0.002 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00270 (23681) covalent geometry : angle 0.60906 (32470) hydrogen bonds : bond 0.06839 ( 1105) hydrogen bonds : angle 4.29280 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 450 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: C 37 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8886 (pt0) REVERT: D 33 GLU cc_start: 0.9581 (tp30) cc_final: 0.9316 (mm-30) REVERT: D 34 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8834 (mmp80) REVERT: D 37 GLU cc_start: 0.9262 (pt0) cc_final: 0.8929 (pt0) REVERT: D 63 THR cc_start: 0.9199 (p) cc_final: 0.8846 (m) REVERT: D 119 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7335 (mptt) REVERT: D 157 GLU cc_start: 0.8897 (tt0) cc_final: 0.8644 (tt0) REVERT: D 176 ILE cc_start: 0.8378 (mm) cc_final: 0.8127 (mt) REVERT: D 180 ASN cc_start: 0.7501 (m110) cc_final: 0.7188 (m110) REVERT: I 37 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9083 (pt0) REVERT: I 45 GLU cc_start: 0.8579 (mp0) cc_final: 0.8349 (tp30) REVERT: J 33 GLU cc_start: 0.9636 (tp30) cc_final: 0.9306 (mm-30) REVERT: J 37 GLU cc_start: 0.9294 (pt0) cc_final: 0.8874 (pt0) REVERT: J 44 SER cc_start: 0.9342 (m) cc_final: 0.9105 (p) REVERT: J 119 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7178 (mptt) REVERT: J 157 GLU cc_start: 0.8920 (tt0) cc_final: 0.8689 (tt0) REVERT: J 180 ASN cc_start: 0.8166 (m110) cc_final: 0.7707 (m110) REVERT: K 33 GLU cc_start: 0.9498 (tp30) cc_final: 0.8810 (tm-30) REVERT: K 37 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8666 (pt0) REVERT: K 45 GLU cc_start: 0.8653 (mp0) cc_final: 0.8244 (mp0) REVERT: K 48 SER cc_start: 0.9131 (m) cc_final: 0.8872 (p) REVERT: N 33 GLU cc_start: 0.9467 (tm-30) cc_final: 0.9042 (tp30) REVERT: N 37 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8973 (pt0) REVERT: N 113 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.8035 (m) REVERT: O 45 GLU cc_start: 0.8619 (mp0) cc_final: 0.8176 (tp30) REVERT: O 48 SER cc_start: 0.9236 (m) cc_final: 0.8734 (p) REVERT: P 33 GLU cc_start: 0.9449 (tm-30) cc_final: 0.8955 (tp30) REVERT: P 37 GLU cc_start: 0.9137 (pt0) cc_final: 0.8710 (pt0) REVERT: Q 180 ASN cc_start: 0.8591 (m110) cc_final: 0.8131 (m110) REVERT: R 33 GLU cc_start: 0.9513 (tp30) cc_final: 0.8783 (tm-30) REVERT: R 34 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5524 (mmm-85) REVERT: R 37 GLU cc_start: 0.8994 (pt0) cc_final: 0.8623 (pt0) REVERT: R 45 GLU cc_start: 0.8771 (mp0) cc_final: 0.8340 (mp0) REVERT: S 33 GLU cc_start: 0.9605 (tp30) cc_final: 0.9300 (mm-30) REVERT: S 44 SER cc_start: 0.9336 (m) cc_final: 0.9055 (p) REVERT: S 61 GLU cc_start: 0.9446 (pt0) cc_final: 0.8612 (pm20) REVERT: S 119 LYS cc_start: 0.7988 (mmmm) cc_final: 0.6995 (mptt) REVERT: S 180 ASN cc_start: 0.8564 (m110) cc_final: 0.8118 (m110) outliers start: 117 outliers final: 72 residues processed: 526 average time/residue: 0.6559 time to fit residues: 394.1187 Evaluate side-chains 475 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 397 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 224 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 289 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062043 restraints weight = 57485.101| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.14 r_work: 0.2725 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23681 Z= 0.194 Angle : 0.715 16.148 32470 Z= 0.353 Chirality : 0.048 0.143 4165 Planarity : 0.005 0.055 4131 Dihedral : 3.993 21.276 3264 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.37 % Allowed : 20.90 % Favored : 74.73 % 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: 0.42 (0.15), residues: 3077 helix: 3.88 (0.17), residues: 646 sheet: 0.27 (0.17), residues: 1071 loop : -1.60 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 34 TYR 0.013 0.001 TYR K 40 PHE 0.011 0.002 PHE O 30 TRP 0.003 0.001 TRP J 112 HIS 0.002 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00449 (23681) covalent geometry : angle 0.71502 (32470) hydrogen bonds : bond 0.07649 ( 1105) hydrogen bonds : angle 4.54236 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 365 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: C 33 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8243 (pp20) REVERT: C 37 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8949 (pt0) REVERT: C 45 GLU cc_start: 0.8846 (mp0) cc_final: 0.8411 (mp0) REVERT: D 33 GLU cc_start: 0.9600 (tp30) cc_final: 0.9331 (mm-30) REVERT: D 34 ARG cc_start: 0.9147 (tpp-160) cc_final: 0.8913 (mmp80) REVERT: D 37 GLU cc_start: 0.9293 (pt0) cc_final: 0.8953 (pt0) REVERT: D 119 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7363 (mptt) REVERT: D 157 GLU cc_start: 0.8927 (tt0) cc_final: 0.8666 (tt0) REVERT: D 180 ASN cc_start: 0.7509 (m110) cc_final: 0.7128 (m110) REVERT: I 45 GLU cc_start: 0.8595 (mp0) cc_final: 0.8357 (tp30) REVERT: J 33 GLU cc_start: 0.9647 (tp30) cc_final: 0.9389 (mm-30) REVERT: J 37 GLU cc_start: 0.9322 (pt0) cc_final: 0.8913 (pt0) REVERT: J 119 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7146 (mptt) REVERT: J 157 GLU cc_start: 0.8979 (tt0) cc_final: 0.8751 (tt0) REVERT: J 180 ASN cc_start: 0.8170 (m110) cc_final: 0.7710 (m110) REVERT: K 33 GLU cc_start: 0.9550 (tp30) cc_final: 0.8865 (tm-30) REVERT: K 37 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8876 (pt0) REVERT: K 45 GLU cc_start: 0.8655 (mp0) cc_final: 0.8363 (mp0) REVERT: N 33 GLU cc_start: 0.9517 (tm-30) cc_final: 0.9091 (tp30) REVERT: N 37 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.9001 (pt0) REVERT: O 45 GLU cc_start: 0.8675 (mp0) cc_final: 0.8426 (tp30) REVERT: O 48 SER cc_start: 0.9387 (m) cc_final: 0.9129 (m) REVERT: P 33 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9066 (tp30) REVERT: P 37 GLU cc_start: 0.9192 (pt0) cc_final: 0.8787 (pt0) REVERT: R 33 GLU cc_start: 0.9536 (tp30) cc_final: 0.8864 (tm-30) REVERT: R 34 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.5452 (mmm-85) REVERT: R 45 GLU cc_start: 0.8814 (mp0) cc_final: 0.8374 (mp0) REVERT: S 33 GLU cc_start: 0.9601 (tp30) cc_final: 0.9350 (mm-30) REVERT: S 37 GLU cc_start: 0.9232 (pt0) cc_final: 0.9032 (pt0) REVERT: S 119 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7014 (mptt) REVERT: S 180 ASN cc_start: 0.8532 (m110) cc_final: 0.8065 (m110) outliers start: 113 outliers final: 80 residues processed: 450 average time/residue: 0.7275 time to fit residues: 368.7470 Evaluate side-chains 445 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 361 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 169 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 169 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 6 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 295 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.076744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.061825 restraints weight = 57125.955| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 4.12 r_work: 0.2719 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 23681 Z= 0.203 Angle : 0.736 19.239 32470 Z= 0.363 Chirality : 0.048 0.164 4165 Planarity : 0.005 0.057 4131 Dihedral : 4.072 20.906 3264 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.53 % Allowed : 21.21 % Favored : 74.26 % 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: 0.36 (0.15), residues: 3077 helix: 3.78 (0.17), residues: 646 sheet: 0.26 (0.17), residues: 1071 loop : -1.62 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 34 TYR 0.011 0.001 TYR E 40 PHE 0.032 0.002 PHE D 20 TRP 0.003 0.001 TRP C 116 HIS 0.002 0.001 HIS S 107 Details of bonding type rmsd covalent geometry : bond 0.00470 (23681) covalent geometry : angle 0.73566 (32470) hydrogen bonds : bond 0.07814 ( 1105) hydrogen bonds : angle 4.61073 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 359 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: C 33 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8031 (pp20) REVERT: C 37 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: C 45 GLU cc_start: 0.8854 (mp0) cc_final: 0.8432 (mp0) REVERT: D 33 GLU cc_start: 0.9600 (tp30) cc_final: 0.9325 (mm-30) REVERT: D 34 ARG cc_start: 0.9211 (tpp-160) cc_final: 0.8934 (mmp80) REVERT: D 37 GLU cc_start: 0.9303 (pt0) cc_final: 0.8956 (pt0) REVERT: D 119 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7376 (mptt) REVERT: D 157 GLU cc_start: 0.8931 (tt0) cc_final: 0.8674 (tt0) REVERT: D 180 ASN cc_start: 0.7545 (m110) cc_final: 0.7162 (m110) REVERT: G 37 GLU cc_start: 0.9442 (tp30) cc_final: 0.9209 (tt0) REVERT: I 45 GLU cc_start: 0.8598 (mp0) cc_final: 0.8349 (tp30) REVERT: J 33 GLU cc_start: 0.9647 (tp30) cc_final: 0.9430 (mm-30) REVERT: J 37 GLU cc_start: 0.9327 (pt0) cc_final: 0.9076 (pt0) REVERT: J 119 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7216 (mptt) REVERT: J 157 GLU cc_start: 0.8981 (tt0) cc_final: 0.8756 (tt0) REVERT: J 180 ASN cc_start: 0.8167 (m110) cc_final: 0.7706 (m110) REVERT: K 33 GLU cc_start: 0.9544 (tp30) cc_final: 0.8861 (tm-30) REVERT: K 37 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8876 (pt0) REVERT: K 45 GLU cc_start: 0.8677 (mp0) cc_final: 0.8418 (mp0) REVERT: N 33 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9038 (tp30) REVERT: N 37 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.8910 (pt0) REVERT: O 45 GLU cc_start: 0.8656 (mp0) cc_final: 0.8401 (tp30) REVERT: O 48 SER cc_start: 0.9401 (m) cc_final: 0.9145 (m) REVERT: P 33 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9058 (tp30) REVERT: P 37 GLU cc_start: 0.9190 (pt0) cc_final: 0.8901 (pt0) REVERT: R 33 GLU cc_start: 0.9567 (tp30) cc_final: 0.8890 (tm-30) REVERT: R 34 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5468 (mmm-85) REVERT: R 45 GLU cc_start: 0.8832 (mp0) cc_final: 0.8405 (mp0) REVERT: R 128 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8908 (m) REVERT: S 33 GLU cc_start: 0.9605 (tp30) cc_final: 0.9353 (mm-30) REVERT: S 37 GLU cc_start: 0.9233 (pt0) cc_final: 0.9010 (pt0) REVERT: S 119 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7046 (mptt) REVERT: S 180 ASN cc_start: 0.8528 (m110) cc_final: 0.8057 (m110) outliers start: 117 outliers final: 87 residues processed: 453 average time/residue: 0.6861 time to fit residues: 350.6578 Evaluate side-chains 426 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 334 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 169 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 169 GLN Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 169 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 181 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 259 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 293 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.081477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066001 restraints weight = 56155.099| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.26 r_work: 0.2807 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23681 Z= 0.140 Angle : 0.706 20.439 32470 Z= 0.341 Chirality : 0.047 0.154 4165 Planarity : 0.004 0.056 4131 Dihedral : 3.784 18.813 3264 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.10 % Allowed : 21.83 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3077 helix: 3.99 (0.17), residues: 646 sheet: 0.33 (0.17), residues: 1054 loop : -1.52 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 34 TYR 0.009 0.001 TYR E 40 PHE 0.015 0.001 PHE E 30 TRP 0.003 0.000 TRP J 112 HIS 0.001 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00291 (23681) covalent geometry : angle 0.70606 (32470) hydrogen bonds : bond 0.06800 ( 1105) hydrogen bonds : angle 4.31266 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 438 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: C 33 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8089 (pp20) REVERT: C 37 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8853 (pt0) REVERT: D 33 GLU cc_start: 0.9599 (tp30) cc_final: 0.9376 (mm-30) REVERT: D 37 GLU cc_start: 0.9258 (pt0) cc_final: 0.8786 (pt0) REVERT: D 63 THR cc_start: 0.9207 (p) cc_final: 0.8881 (m) REVERT: D 119 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7379 (mptt) REVERT: D 157 GLU cc_start: 0.8880 (tt0) cc_final: 0.8618 (tt0) REVERT: D 180 ASN cc_start: 0.7479 (m110) cc_final: 0.7169 (m110) REVERT: E 33 GLU cc_start: 0.9630 (tp30) cc_final: 0.9430 (mm-30) REVERT: G 37 GLU cc_start: 0.9420 (tp30) cc_final: 0.9154 (tt0) REVERT: G 83 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8715 (tp30) REVERT: H 83 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8529 (tp30) REVERT: J 33 GLU cc_start: 0.9651 (tp30) cc_final: 0.9416 (mm-30) REVERT: J 37 GLU cc_start: 0.9309 (pt0) cc_final: 0.8840 (pt0) REVERT: J 119 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7210 (mptt) REVERT: J 157 GLU cc_start: 0.8935 (tt0) cc_final: 0.8718 (tt0) REVERT: J 180 ASN cc_start: 0.8116 (m110) cc_final: 0.7669 (m110) REVERT: K 33 GLU cc_start: 0.9503 (tp30) cc_final: 0.8776 (tm-30) REVERT: K 37 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8695 (pt0) REVERT: K 45 GLU cc_start: 0.8681 (mp0) cc_final: 0.8326 (mp0) REVERT: K 48 SER cc_start: 0.9111 (m) cc_final: 0.8853 (p) REVERT: N 33 GLU cc_start: 0.9510 (tm-30) cc_final: 0.8947 (tp30) REVERT: N 37 GLU cc_start: 0.9225 (pt0) cc_final: 0.8738 (pt0) REVERT: O 37 GLU cc_start: 0.9454 (tt0) cc_final: 0.9090 (pt0) REVERT: O 45 GLU cc_start: 0.8632 (mp0) cc_final: 0.8417 (tp30) REVERT: O 48 SER cc_start: 0.9198 (m) cc_final: 0.8922 (m) REVERT: P 33 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9006 (tp30) REVERT: P 37 GLU cc_start: 0.9167 (pt0) cc_final: 0.8849 (pt0) REVERT: P 83 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8664 (tp30) REVERT: Q 83 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8647 (tp30) REVERT: Q 180 ASN cc_start: 0.8599 (m110) cc_final: 0.8156 (m110) REVERT: R 33 GLU cc_start: 0.9504 (tp30) cc_final: 0.8814 (tm-30) REVERT: R 34 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.5537 (mmm-85) REVERT: R 37 GLU cc_start: 0.8941 (pt0) cc_final: 0.8493 (pt0) REVERT: R 45 GLU cc_start: 0.8765 (mp0) cc_final: 0.8434 (tp30) REVERT: R 128 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8913 (m) REVERT: S 33 GLU cc_start: 0.9590 (tp30) cc_final: 0.9331 (mm-30) REVERT: S 37 GLU cc_start: 0.9211 (pt0) cc_final: 0.8976 (pt0) REVERT: S 61 GLU cc_start: 0.9484 (pt0) cc_final: 0.8665 (pm20) REVERT: S 119 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7036 (mptt) REVERT: S 153 ASP cc_start: 0.9054 (p0) cc_final: 0.8728 (m-30) REVERT: S 180 ASN cc_start: 0.8403 (m110) cc_final: 0.7948 (m110) outliers start: 106 outliers final: 72 residues processed: 509 average time/residue: 0.6022 time to fit residues: 349.9699 Evaluate side-chains 473 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 397 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 169 GLN Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 169 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.076408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.061628 restraints weight = 57310.131| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.09 r_work: 0.2716 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 23681 Z= 0.234 Angle : 0.832 21.368 32470 Z= 0.400 Chirality : 0.049 0.175 4165 Planarity : 0.005 0.059 4131 Dihedral : 4.084 22.075 3264 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.52 % Allowed : 22.72 % Favored : 73.76 % 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: 0.52 (0.15), residues: 3077 helix: 3.63 (0.17), residues: 646 sheet: 1.11 (0.17), residues: 935 loop : -1.82 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 34 TYR 0.010 0.001 TYR G 40 PHE 0.030 0.002 PHE D 20 TRP 0.003 0.001 TRP C 112 HIS 0.002 0.001 HIS S 107 Details of bonding type rmsd covalent geometry : bond 0.00555 (23681) covalent geometry : angle 0.83157 (32470) hydrogen bonds : bond 0.07895 ( 1105) hydrogen bonds : angle 4.68687 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 348 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7943 (pp20) REVERT: C 37 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8767 (pt0) REVERT: C 45 GLU cc_start: 0.8871 (mp0) cc_final: 0.8431 (mp0) REVERT: D 33 GLU cc_start: 0.9644 (tp30) cc_final: 0.9421 (mm-30) REVERT: D 37 GLU cc_start: 0.9293 (pt0) cc_final: 0.9090 (pt0) REVERT: D 119 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7377 (mptt) REVERT: D 157 GLU cc_start: 0.8936 (tt0) cc_final: 0.8677 (tt0) REVERT: D 180 ASN cc_start: 0.7520 (m110) cc_final: 0.7159 (m110) REVERT: E 45 GLU cc_start: 0.8931 (pm20) cc_final: 0.8590 (mp0) REVERT: G 37 GLU cc_start: 0.9457 (tp30) cc_final: 0.9174 (tt0) REVERT: J 33 GLU cc_start: 0.9646 (tp30) cc_final: 0.9426 (mm-30) REVERT: J 37 GLU cc_start: 0.9328 (pt0) cc_final: 0.9052 (pt0) REVERT: J 119 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7262 (mptt) REVERT: J 157 GLU cc_start: 0.8954 (tt0) cc_final: 0.8652 (tt0) REVERT: J 180 ASN cc_start: 0.8133 (m110) cc_final: 0.7681 (m110) REVERT: K 33 GLU cc_start: 0.9571 (tp30) cc_final: 0.8862 (tm-30) REVERT: K 37 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8851 (pt0) REVERT: N 37 GLU cc_start: 0.9321 (pt0) cc_final: 0.9056 (pt0) REVERT: O 37 GLU cc_start: 0.9480 (tt0) cc_final: 0.9147 (pt0) REVERT: O 45 GLU cc_start: 0.8650 (mp0) cc_final: 0.8398 (tp30) REVERT: O 48 SER cc_start: 0.9381 (m) cc_final: 0.9092 (m) REVERT: P 33 GLU cc_start: 0.9516 (tm-30) cc_final: 0.9059 (tp30) REVERT: P 37 GLU cc_start: 0.9236 (pt0) cc_final: 0.8987 (pt0) REVERT: Q 37 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8656 (pt0) REVERT: R 33 GLU cc_start: 0.9576 (tp30) cc_final: 0.8892 (tm-30) REVERT: R 34 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.5470 (mmm-85) REVERT: R 45 GLU cc_start: 0.8821 (mp0) cc_final: 0.8378 (mp0) REVERT: R 128 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8776 (m) REVERT: S 33 GLU cc_start: 0.9606 (tp30) cc_final: 0.9329 (mm-30) REVERT: S 119 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7061 (mptt) REVERT: S 180 ASN cc_start: 0.8428 (m110) cc_final: 0.7925 (m110) outliers start: 91 outliers final: 73 residues processed: 425 average time/residue: 0.6962 time to fit residues: 333.4705 Evaluate side-chains 416 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 338 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 165 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.078908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.063697 restraints weight = 56765.993| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.21 r_work: 0.2759 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 23681 Z= 0.163 Angle : 0.801 21.251 32470 Z= 0.377 Chirality : 0.048 0.179 4165 Planarity : 0.005 0.056 4131 Dihedral : 3.942 19.386 3264 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.52 % Allowed : 22.91 % Favored : 73.57 % 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: 0.44 (0.15), residues: 3077 helix: 3.75 (0.17), residues: 646 sheet: 0.35 (0.16), residues: 1071 loop : -1.58 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 34 TYR 0.016 0.001 TYR P 40 PHE 0.020 0.001 PHE S 154 TRP 0.004 0.001 TRP J 112 HIS 0.002 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00359 (23681) covalent geometry : angle 0.80080 (32470) hydrogen bonds : bond 0.07439 ( 1105) hydrogen bonds : angle 4.53873 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9252.17 seconds wall clock time: 157 minutes 56.15 seconds (9476.15 seconds total)