Starting phenix.real_space_refine on Wed Jun 11 08:44:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo0_32637/06_2025/7wo0_32637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo0_32637/06_2025/7wo0_32637.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/7wo0_32637/06_2025/7wo0_32637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo0_32637/06_2025/7wo0_32637.map" model { file = "/net/cci-nas-00/data/ceres_data/7wo0_32637/06_2025/7wo0_32637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo0_32637/06_2025/7wo0_32637.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 3948 2.51 5 N 1092 2.21 5 O 1302 1.98 5 H 6622 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12964 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Restraints were copied for chains: C, B, E, D, G, F, O, Q, P, S, R, U, T Time building chain proxies: 3.39, per 1000 atoms: 0.26 Number of scatterers: 12964 At special positions: 0 Unit cell: (100.43, 110.39, 54.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 1302 8.00 N 1092 7.00 C 3948 6.00 H 6622 1.00 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: 3.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.382A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY B 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS B 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER A 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY F 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL E 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LYS F 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER E 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS G 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER F 42 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 57 removed outlier: 6.834A pdb=" N VAL A 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS A 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLY C 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N HIS B 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N VAL C 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N VAL B 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR B 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA B 56 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS C 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY D 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL D 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL E 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS D 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY E 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL E 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS E 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY F 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL F 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL G 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS F 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY G 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.338A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR E 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR F 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 72 removed outlier: 6.456A pdb=" N VAL C 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.547A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL E 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL F 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.243A pdb=" N VAL C 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.854A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE E 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98 removed outlier: 6.793A pdb=" N GLY A 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR C 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL B 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE C 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LYS B 97 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS C 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY C 93 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 93 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY E 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY F 93 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 37 through 44 removed outlier: 6.381A pdb=" N LEU O 38 " --> pdb=" O TYR P 39 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY P 41 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL O 40 " --> pdb=" O GLY P 41 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS P 43 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER O 42 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU P 38 " --> pdb=" O TYR Q 39 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY Q 41 " --> pdb=" O LEU P 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL P 40 " --> pdb=" O GLY Q 41 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LYS Q 43 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER P 42 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU Q 38 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLY R 41 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL Q 40 " --> pdb=" O GLY R 41 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LYS R 43 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER Q 42 " --> pdb=" O LYS R 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU R 38 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY S 41 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL R 40 " --> pdb=" O GLY S 41 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS S 43 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER R 42 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU S 38 " --> pdb=" O TYR T 39 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY T 41 " --> pdb=" O LEU S 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL S 40 " --> pdb=" O GLY T 41 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LYS T 43 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER S 42 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU T 38 " --> pdb=" O TYR U 39 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY U 41 " --> pdb=" O LEU T 38 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL T 40 " --> pdb=" O GLY U 41 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS U 43 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER T 42 " --> pdb=" O LYS U 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 47 through 57 removed outlier: 6.835A pdb=" N VAL O 48 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL P 49 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS O 50 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY P 51 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL P 48 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL Q 49 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS P 50 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY Q 51 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL Q 48 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLY R 51 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS Q 50 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N THR R 53 " --> pdb=" O HIS Q 50 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL Q 52 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL R 55 " --> pdb=" O VAL Q 52 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR Q 54 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLU R 57 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA Q 56 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL R 48 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL S 49 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS R 50 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY S 51 " --> pdb=" O HIS R 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL S 48 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL T 49 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS S 50 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY T 51 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL T 48 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL U 49 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS T 50 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY U 51 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 63 through 66 removed outlier: 6.337A pdb=" N THR O 64 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR P 64 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR Q 64 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR R 64 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR S 64 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR T 64 " --> pdb=" O ASN U 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 70 through 72 Processing sheet with id=AB4, first strand: chain 'O' and resid 77 through 78 removed outlier: 6.547A pdb=" N VAL O 77 " --> pdb=" O ALA P 78 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL P 77 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL Q 77 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL R 77 " --> pdb=" O ALA S 78 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL S 77 " --> pdb=" O ALA T 78 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL T 77 " --> pdb=" O ALA U 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'O' and resid 81 through 83 Processing sheet with id=AB6, first strand: chain 'O' and resid 88 through 89 removed outlier: 6.854A pdb=" N ILE O 88 " --> pdb=" O ALA P 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE P 88 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE Q 88 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE R 88 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE S 88 " --> pdb=" O ALA T 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE T 88 " --> pdb=" O ALA U 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 92 through 98 removed outlier: 6.793A pdb=" N GLY O 93 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY P 93 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY Q 93 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY R 93 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY S 93 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY T 93 " --> pdb=" O THR U 92 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 531 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: 5.00 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.00: 392 1.00 - 1.14: 6230 1.14 - 1.28: 1134 1.28 - 1.41: 1204 1.41 - 1.55: 4032 Bond restraints: 12992 Sorted by residual: bond pdb=" N GLU D 61 " pdb=" H GLU D 61 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" ND2 ASN F 65 " pdb="HD22 ASN F 65 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU P 61 " pdb=" H GLU P 61 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR P 81 " pdb=" H THR P 81 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR Q 54 " pdb=" H THR Q 54 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 12987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21446 2.07 - 4.14: 356 4.14 - 6.21: 1788 6.21 - 8.28: 14 8.28 - 10.35: 28 Bond angle restraints: 23632 Sorted by residual: angle pdb=" C ASP Q 98 " pdb=" CA ASP Q 98 " pdb=" CB ASP Q 98 " ideal model delta sigma weight residual 110.42 118.66 -8.24 1.99e+00 2.53e-01 1.71e+01 angle pdb=" C ASP U 98 " pdb=" CA ASP U 98 " pdb=" CB ASP U 98 " ideal model delta sigma weight residual 110.42 118.63 -8.21 1.99e+00 2.53e-01 1.70e+01 angle pdb=" C ASP O 98 " pdb=" CA ASP O 98 " pdb=" CB ASP O 98 " ideal model delta sigma weight residual 110.42 118.62 -8.20 1.99e+00 2.53e-01 1.70e+01 angle pdb=" C ASP S 98 " pdb=" CA ASP S 98 " pdb=" CB ASP S 98 " ideal model delta sigma weight residual 110.42 118.62 -8.20 1.99e+00 2.53e-01 1.70e+01 angle pdb=" C ASP C 98 " pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " ideal model delta sigma weight residual 110.42 118.61 -8.19 1.99e+00 2.53e-01 1.69e+01 ... (remaining 23627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4956 17.77 - 35.53: 322 35.53 - 53.30: 252 53.30 - 71.06: 392 71.06 - 88.83: 14 Dihedral angle restraints: 5936 sinusoidal: 3318 harmonic: 2618 Sorted by residual: dihedral pdb=" CA LYS A 45 " pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " pdb=" CD LYS A 45 " ideal model delta sinusoidal sigma weight residual -60.00 -117.75 57.75 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS D 45 " pdb=" CB LYS D 45 " pdb=" CG LYS D 45 " pdb=" CD LYS D 45 " ideal model delta sinusoidal sigma weight residual -60.00 -117.75 57.75 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS P 45 " pdb=" CB LYS P 45 " pdb=" CG LYS P 45 " pdb=" CD LYS P 45 " ideal model delta sinusoidal sigma weight residual -60.00 -117.74 57.74 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 444 0.027 - 0.053: 320 0.053 - 0.080: 100 0.080 - 0.107: 179 0.107 - 0.133: 77 Chirality restraints: 1120 Sorted by residual: chirality pdb=" CA VAL P 95 " pdb=" N VAL P 95 " pdb=" C VAL P 95 " pdb=" CB VAL P 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL S 95 " pdb=" N VAL S 95 " pdb=" C VAL S 95 " pdb=" CB VAL S 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL F 95 " pdb=" N VAL F 95 " pdb=" C VAL F 95 " pdb=" CB VAL F 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1117 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 99 " 0.030 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN A 99 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 99 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN A 99 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 99 " -0.760 2.00e-02 2.50e+03 pdb="HE22 GLN A 99 " 0.771 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 99 " -0.029 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN S 99 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN S 99 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN S 99 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN S 99 " 0.760 2.00e-02 2.50e+03 pdb="HE22 GLN S 99 " -0.771 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 99 " 0.030 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN B 99 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 99 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN B 99 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 99 " -0.759 2.00e-02 2.50e+03 pdb="HE22 GLN B 99 " 0.770 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.20: 1616 2.20 - 2.77: 24667 2.77 - 3.35: 32275 3.35 - 3.92: 48036 3.92 - 4.50: 65038 Nonbonded interactions: 171632 Sorted by model distance: nonbonded pdb=" OE1 GLU D 35 " pdb=" H3 GLU D 35 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU R 35 " pdb=" H3 GLU R 35 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU E 35 " pdb=" H3 GLU E 35 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU G 35 " pdb=" H3 GLU G 35 " model vdw 1.620 2.450 nonbonded pdb=" OE1 GLU Q 35 " pdb=" H3 GLU Q 35 " model vdw 1.620 2.450 ... (remaining 171627 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'O' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.230 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 27.150 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.007 0.050 6370 Z= 0.398 Angle : 0.905 8.238 8610 Z= 0.530 Chirality : 0.056 0.133 1120 Planarity : 0.005 0.026 1078 Dihedral : 15.451 69.877 2184 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.18), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.14), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.022 0.006 PHE A 94 TYR 0.033 0.009 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.16223 ( 177) hydrogen bonds : angle 8.53851 ( 531) covalent geometry : bond 0.00727 ( 6370) covalent geometry : angle 0.90538 ( 8610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7955 (tttp) REVERT: T 60 LYS cc_start: 0.8171 (mttt) cc_final: 0.7864 (mtpt) REVERT: T 61 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8060 (mt-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 3.4689 time to fit residues: 284.7439 Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.167001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.122340 restraints weight = 19290.896| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.50 r_work: 0.3809 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 6370 Z= 0.137 Angle : 0.486 4.431 8610 Z= 0.278 Chirality : 0.055 0.128 1120 Planarity : 0.002 0.010 1078 Dihedral : 4.650 15.847 910 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.017 0.004 PHE P 94 TYR 0.003 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 177) hydrogen bonds : angle 6.07858 ( 531) covalent geometry : bond 0.00257 ( 6370) covalent geometry : angle 0.48597 ( 8610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7571 (tmtm) REVERT: D 45 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7850 (tmtt) REVERT: D 60 LYS cc_start: 0.8365 (mttt) cc_final: 0.7911 (mtpp) REVERT: E 45 LYS cc_start: 0.8187 (tmtt) cc_final: 0.7831 (tttp) REVERT: G 60 LYS cc_start: 0.8510 (mttt) cc_final: 0.7979 (mtpt) REVERT: R 60 LYS cc_start: 0.8315 (mttt) cc_final: 0.7890 (mtpt) REVERT: S 45 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7751 (tttp) REVERT: T 60 LYS cc_start: 0.8382 (mttt) cc_final: 0.7885 (mtpt) REVERT: U 60 LYS cc_start: 0.8357 (mttt) cc_final: 0.7798 (mtpt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 4.3273 time to fit residues: 294.8653 Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 79 GLN D 79 GLN E 79 GLN F 79 GLN G 79 GLN P 79 GLN Q 79 GLN T 79 GLN U 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.164753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.119081 restraints weight = 19596.477| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.57 r_work: 0.3767 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 6370 Z= 0.203 Angle : 0.499 4.433 8610 Z= 0.288 Chirality : 0.055 0.131 1120 Planarity : 0.002 0.009 1078 Dihedral : 4.930 15.324 910 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.30 % Allowed : 11.25 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.020 0.005 PHE D 94 TYR 0.002 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 177) hydrogen bonds : angle 5.86310 ( 531) covalent geometry : bond 0.00379 ( 6370) covalent geometry : angle 0.49917 ( 8610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.037 Fit side-chains REVERT: C 45 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7577 (tmtm) REVERT: C 60 LYS cc_start: 0.8170 (mttt) cc_final: 0.7744 (mtpp) REVERT: D 60 LYS cc_start: 0.8351 (mttt) cc_final: 0.7864 (mtpp) REVERT: G 60 LYS cc_start: 0.8521 (mttt) cc_final: 0.7947 (mtpt) REVERT: Q 60 LYS cc_start: 0.8260 (mttt) cc_final: 0.7783 (mtpp) REVERT: R 60 LYS cc_start: 0.8421 (mttt) cc_final: 0.7915 (mtpt) REVERT: S 45 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7759 (tttp) REVERT: T 60 LYS cc_start: 0.8444 (mttt) cc_final: 0.7928 (mtpt) REVERT: U 60 LYS cc_start: 0.8352 (mttt) cc_final: 0.7761 (mtpt) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 4.2465 time to fit residues: 285.7873 Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.164989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.119891 restraints weight = 19679.968| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.56 r_work: 0.3789 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6370 Z= 0.218 Angle : 0.497 4.324 8610 Z= 0.286 Chirality : 0.055 0.125 1120 Planarity : 0.002 0.009 1078 Dihedral : 4.976 15.910 910 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.30 % Allowed : 12.16 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 50 PHE 0.019 0.005 PHE D 94 TYR 0.002 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 177) hydrogen bonds : angle 5.80079 ( 531) covalent geometry : bond 0.00412 ( 6370) covalent geometry : angle 0.49683 ( 8610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.915 Fit side-chains REVERT: C 45 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7588 (tmtm) REVERT: C 60 LYS cc_start: 0.8251 (mttt) cc_final: 0.7813 (mtpp) REVERT: D 60 LYS cc_start: 0.8401 (mttt) cc_final: 0.7958 (mtpp) REVERT: G 60 LYS cc_start: 0.8619 (mttt) cc_final: 0.8102 (mtpt) REVERT: Q 60 LYS cc_start: 0.8252 (mttt) cc_final: 0.7821 (mtpp) REVERT: R 60 LYS cc_start: 0.8477 (mttt) cc_final: 0.8040 (mtpt) REVERT: S 45 LYS cc_start: 0.8123 (tmtt) cc_final: 0.7787 (tttp) REVERT: T 60 LYS cc_start: 0.8504 (mttt) cc_final: 0.8014 (mtpt) REVERT: U 60 LYS cc_start: 0.8415 (mttt) cc_final: 0.7809 (mtpt) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 4.0454 time to fit residues: 271.8921 Evaluate side-chains 63 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.163937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.118437 restraints weight = 19901.687| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.60 r_work: 0.3769 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6370 Z= 0.280 Angle : 0.537 5.016 8610 Z= 0.309 Chirality : 0.055 0.130 1120 Planarity : 0.002 0.010 1078 Dihedral : 5.271 16.374 910 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.46 % Allowed : 12.46 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 50 PHE 0.022 0.006 PHE D 94 TYR 0.002 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 177) hydrogen bonds : angle 5.86397 ( 531) covalent geometry : bond 0.00537 ( 6370) covalent geometry : angle 0.53660 ( 8610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 1.004 Fit side-chains REVERT: C 45 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7657 (tmtm) REVERT: C 60 LYS cc_start: 0.8292 (mttt) cc_final: 0.7842 (mtpp) REVERT: D 60 LYS cc_start: 0.8427 (mttt) cc_final: 0.7962 (mtpp) REVERT: F 60 LYS cc_start: 0.8489 (mttt) cc_final: 0.8093 (mtpt) REVERT: G 60 LYS cc_start: 0.8632 (mttt) cc_final: 0.8105 (mtpt) REVERT: Q 60 LYS cc_start: 0.8336 (mttt) cc_final: 0.7826 (mtpp) REVERT: R 60 LYS cc_start: 0.8516 (mttt) cc_final: 0.8093 (mtpt) REVERT: S 45 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7798 (tttp) REVERT: T 60 LYS cc_start: 0.8567 (mttt) cc_final: 0.8067 (mtpt) REVERT: U 60 LYS cc_start: 0.8454 (mttt) cc_final: 0.7842 (mtpt) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 4.4204 time to fit residues: 293.0726 Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.164580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119572 restraints weight = 19909.442| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.57 r_work: 0.3782 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 6370 Z= 0.247 Angle : 0.501 4.529 8610 Z= 0.290 Chirality : 0.055 0.125 1120 Planarity : 0.002 0.009 1078 Dihedral : 5.128 16.456 910 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.61 % Allowed : 12.01 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.020 0.005 PHE D 94 TYR 0.002 0.001 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 177) hydrogen bonds : angle 5.75175 ( 531) covalent geometry : bond 0.00473 ( 6370) covalent geometry : angle 0.50104 ( 8610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.005 Fit side-chains REVERT: C 45 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7583 (tmtm) REVERT: C 60 LYS cc_start: 0.8260 (mttt) cc_final: 0.7820 (mtpp) REVERT: D 60 LYS cc_start: 0.8416 (mttt) cc_final: 0.7966 (mtpp) REVERT: F 60 LYS cc_start: 0.8476 (mttt) cc_final: 0.8085 (mtpt) REVERT: G 60 LYS cc_start: 0.8674 (mttt) cc_final: 0.8137 (mtpt) REVERT: Q 60 LYS cc_start: 0.8337 (mttt) cc_final: 0.7854 (mtpp) REVERT: R 60 LYS cc_start: 0.8477 (mttt) cc_final: 0.8037 (mtpt) REVERT: S 45 LYS cc_start: 0.8082 (tmtt) cc_final: 0.7816 (tttp) REVERT: T 60 LYS cc_start: 0.8557 (mttt) cc_final: 0.8066 (mtpt) REVERT: U 60 LYS cc_start: 0.8462 (mttt) cc_final: 0.7855 (mtpt) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 4.6586 time to fit residues: 302.7676 Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.165847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.121593 restraints weight = 19741.848| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.51 r_work: 0.3812 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 6370 Z= 0.138 Angle : 0.431 4.166 8610 Z= 0.253 Chirality : 0.054 0.125 1120 Planarity : 0.002 0.008 1078 Dihedral : 4.667 16.103 910 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.30 % Allowed : 12.92 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 PHE 0.017 0.004 PHE D 94 TYR 0.002 0.000 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 177) hydrogen bonds : angle 5.46167 ( 531) covalent geometry : bond 0.00250 ( 6370) covalent geometry : angle 0.43148 ( 8610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.289 Fit side-chains REVERT: C 45 LYS cc_start: 0.7955 (tmtt) cc_final: 0.7534 (tmtm) REVERT: C 60 LYS cc_start: 0.8185 (mttt) cc_final: 0.7734 (mtpp) REVERT: D 60 LYS cc_start: 0.8251 (mttt) cc_final: 0.7814 (mtpt) REVERT: G 60 LYS cc_start: 0.8644 (mttt) cc_final: 0.8092 (mtpt) REVERT: R 60 LYS cc_start: 0.8349 (mttt) cc_final: 0.7927 (mtpt) REVERT: T 60 LYS cc_start: 0.8512 (mttt) cc_final: 0.8017 (mtpt) REVERT: U 60 LYS cc_start: 0.8432 (mttt) cc_final: 0.7865 (mtpt) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 4.7572 time to fit residues: 321.2805 Evaluate side-chains 64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.163435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.119229 restraints weight = 19959.756| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.51 r_work: 0.3768 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 6370 Z= 0.304 Angle : 0.538 5.149 8610 Z= 0.311 Chirality : 0.056 0.130 1120 Planarity : 0.002 0.010 1078 Dihedral : 5.222 16.778 910 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.61 % Allowed : 13.37 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.023 0.006 PHE D 94 TYR 0.002 0.000 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 177) hydrogen bonds : angle 5.74269 ( 531) covalent geometry : bond 0.00586 ( 6370) covalent geometry : angle 0.53828 ( 8610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.900 Fit side-chains REVERT: C 45 LYS cc_start: 0.8000 (tmtt) cc_final: 0.7573 (tmtm) REVERT: C 60 LYS cc_start: 0.8211 (mttt) cc_final: 0.7751 (mtpp) REVERT: A 46 GLU cc_start: 0.7642 (tt0) cc_final: 0.7200 (tm-30) REVERT: D 60 LYS cc_start: 0.8367 (mttt) cc_final: 0.7892 (mtpp) REVERT: F 60 LYS cc_start: 0.8441 (mttt) cc_final: 0.8023 (mtpt) REVERT: G 60 LYS cc_start: 0.8643 (mttt) cc_final: 0.8088 (mtpt) REVERT: Q 60 LYS cc_start: 0.8244 (mttt) cc_final: 0.7722 (mtpp) REVERT: R 60 LYS cc_start: 0.8427 (mttt) cc_final: 0.7923 (mtpt) REVERT: S 45 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7845 (tttp) REVERT: T 60 LYS cc_start: 0.8537 (mttt) cc_final: 0.8001 (mtpt) REVERT: U 60 LYS cc_start: 0.8440 (mttt) cc_final: 0.7854 (mtpt) outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 4.4369 time to fit residues: 297.7410 Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.164701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.120380 restraints weight = 19813.969| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.52 r_work: 0.3798 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 6370 Z= 0.200 Angle : 0.475 4.221 8610 Z= 0.275 Chirality : 0.054 0.126 1120 Planarity : 0.002 0.009 1078 Dihedral : 4.954 16.644 910 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.61 % Allowed : 13.53 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 50 PHE 0.019 0.004 PHE D 94 TYR 0.002 0.000 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 177) hydrogen bonds : angle 5.57338 ( 531) covalent geometry : bond 0.00377 ( 6370) covalent geometry : angle 0.47517 ( 8610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.019 Fit side-chains REVERT: C 45 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7544 (tmtm) REVERT: C 60 LYS cc_start: 0.8182 (mttt) cc_final: 0.7738 (mtpp) REVERT: A 46 GLU cc_start: 0.7650 (tt0) cc_final: 0.7193 (tm-30) REVERT: D 60 LYS cc_start: 0.8319 (mttt) cc_final: 0.7864 (mtpp) REVERT: F 60 LYS cc_start: 0.8422 (mttt) cc_final: 0.8009 (mtpt) REVERT: G 60 LYS cc_start: 0.8676 (mttt) cc_final: 0.8110 (mtpt) REVERT: Q 60 LYS cc_start: 0.8205 (mttt) cc_final: 0.7703 (mtpp) REVERT: R 60 LYS cc_start: 0.8381 (mttt) cc_final: 0.7920 (mtpt) REVERT: S 45 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7795 (tttp) REVERT: T 60 LYS cc_start: 0.8540 (mttt) cc_final: 0.8020 (mtpt) REVERT: U 60 LYS cc_start: 0.8444 (mttt) cc_final: 0.7807 (mtpt) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 4.0134 time to fit residues: 270.1317 Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.165651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.121608 restraints weight = 19727.379| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.48 r_work: 0.3820 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 6370 Z= 0.151 Angle : 0.438 4.114 8610 Z= 0.255 Chirality : 0.054 0.125 1120 Planarity : 0.002 0.008 1078 Dihedral : 4.653 16.198 910 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.46 % Allowed : 13.83 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 PHE 0.018 0.004 PHE D 94 TYR 0.002 0.000 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 177) hydrogen bonds : angle 5.39724 ( 531) covalent geometry : bond 0.00277 ( 6370) covalent geometry : angle 0.43792 ( 8610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.979 Fit side-chains REVERT: C 45 LYS cc_start: 0.7950 (tmtt) cc_final: 0.7532 (tmtm) REVERT: C 60 LYS cc_start: 0.8189 (mttt) cc_final: 0.7743 (mtpp) REVERT: D 60 LYS cc_start: 0.8306 (mttt) cc_final: 0.7860 (mtpt) REVERT: G 60 LYS cc_start: 0.8673 (mttt) cc_final: 0.8118 (mtpt) REVERT: G 83 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7449 (mt-10) REVERT: Q 60 LYS cc_start: 0.8210 (mttt) cc_final: 0.7714 (mtpp) REVERT: R 60 LYS cc_start: 0.8364 (mttt) cc_final: 0.7925 (mtpt) REVERT: T 60 LYS cc_start: 0.8537 (mttt) cc_final: 0.8044 (mtpt) REVERT: U 60 LYS cc_start: 0.8438 (mttt) cc_final: 0.7866 (mtpt) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 4.0900 time to fit residues: 262.2172 Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 overall best weight: 1.0592 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.165375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.121334 restraints weight = 19613.343| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.49 r_work: 0.3817 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 6370 Z= 0.154 Angle : 0.442 4.126 8610 Z= 0.257 Chirality : 0.054 0.125 1120 Planarity : 0.002 0.008 1078 Dihedral : 4.658 16.255 910 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.46 % Allowed : 13.83 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.21), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS T 50 PHE 0.018 0.004 PHE D 94 TYR 0.002 0.000 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 177) hydrogen bonds : angle 5.37251 ( 531) covalent geometry : bond 0.00282 ( 6370) covalent geometry : angle 0.44184 ( 8610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10243.50 seconds wall clock time: 179 minutes 5.49 seconds (10745.49 seconds total)