Starting phenix.real_space_refine on Tue Mar 3 15:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ovt_13089/03_2026/7ovt_13089.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ovt_13089/03_2026/7ovt_13089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ovt_13089/03_2026/7ovt_13089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ovt_13089/03_2026/7ovt_13089.map" model { file = "/net/cci-nas-00/data/ceres_data/7ovt_13089/03_2026/7ovt_13089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ovt_13089/03_2026/7ovt_13089.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4212 2.51 5 N 1128 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.61, per 1000 atoms: 0.09 Number of scatterers: 6588 At special positions: 0 Unit cell: (105.04, 127.92, 54.08, 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) S 24 16.00 O 1224 8.00 N 1128 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 294.3 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 58.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 21 removed outlier: 6.752A pdb=" N PHE A 10 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN C 11 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 12 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA C 13 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET A 16 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP C 17 " --> pdb=" O MET A 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE C 10 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN E 11 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY C 12 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA E 13 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET C 16 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP E 17 " --> pdb=" O MET C 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE E 10 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN G 11 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY E 12 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA G 13 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET E 16 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP G 17 " --> pdb=" O MET E 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE G 10 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN I 11 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY G 12 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA I 13 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET G 16 " --> pdb=" O ASP I 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP I 17 " --> pdb=" O MET G 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE I 10 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN K 11 " --> pdb=" O PHE I 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY I 12 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA K 13 " --> pdb=" O GLY I 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET I 16 " --> pdb=" O ASP K 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP K 17 " --> pdb=" O MET I 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.533A pdb=" N LYS A 33 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS C 36 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE A 35 " --> pdb=" O HIS C 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG C 38 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 37 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS C 33 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS E 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE C 35 " --> pdb=" O HIS E 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG E 38 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 37 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS E 33 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS G 36 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE E 35 " --> pdb=" O HIS G 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG G 38 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 37 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS G 33 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS I 36 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE G 35 " --> pdb=" O HIS I 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG I 38 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA G 37 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS I 33 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS K 36 " --> pdb=" O LYS I 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE I 35 " --> pdb=" O HIS K 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG K 38 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA I 37 " --> pdb=" O ARG K 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.879A pdb=" N ALA C 43 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA A 44 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA E 43 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 44 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA G 43 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA E 44 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA I 43 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA G 44 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA K 43 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA I 44 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.214A pdb=" N VAL A 51 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA C 54 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA A 53 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU A 55 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER C 58 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE A 57 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 51 " --> pdb=" O TRP E 52 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA E 54 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA C 53 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU C 55 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER E 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 57 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 51 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA G 54 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA E 53 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU E 55 " --> pdb=" O LYS G 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER G 58 " --> pdb=" O GLU E 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE E 57 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL G 51 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA I 54 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA G 53 " --> pdb=" O ALA I 54 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU G 55 " --> pdb=" O LYS I 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER I 58 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE G 57 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL I 51 " --> pdb=" O TRP K 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA K 54 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA I 53 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS K 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU I 55 " --> pdb=" O LYS K 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER K 58 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE I 57 " --> pdb=" O SER K 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 21 removed outlier: 6.752A pdb=" N PHE B 10 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN D 11 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 12 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA D 13 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 16 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP D 17 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE D 10 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN F 11 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 12 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA F 13 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET D 16 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 17 " --> pdb=" O MET D 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE F 10 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN H 11 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY F 12 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA H 13 " --> pdb=" O GLY F 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET F 16 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP H 17 " --> pdb=" O MET F 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE H 10 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN J 11 " --> pdb=" O PHE H 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY H 12 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA J 13 " --> pdb=" O GLY H 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET H 16 " --> pdb=" O ASP J 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP J 17 " --> pdb=" O MET H 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE J 10 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN L 11 " --> pdb=" O PHE J 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY J 12 " --> pdb=" O GLN L 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA L 13 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET J 16 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 17 " --> pdb=" O MET J 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 38 removed outlier: 6.534A pdb=" N LYS B 33 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS D 36 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 35 " --> pdb=" O HIS D 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG D 38 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 37 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS D 33 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS F 36 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE D 35 " --> pdb=" O HIS F 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG F 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 37 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS F 33 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS H 36 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE F 35 " --> pdb=" O HIS H 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG H 38 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 37 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS H 33 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS J 36 " --> pdb=" O LYS H 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE H 35 " --> pdb=" O HIS J 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG J 38 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA H 37 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS J 33 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS L 36 " --> pdb=" O LYS J 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE J 35 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG L 38 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA J 37 " --> pdb=" O ARG L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 46 removed outlier: 6.879A pdb=" N ALA D 43 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 44 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA F 43 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA D 44 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA H 43 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA F 44 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA J 43 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA H 44 " --> pdb=" O ALA J 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA L 43 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA J 44 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 58 removed outlier: 6.214A pdb=" N VAL B 51 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA D 54 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA B 53 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU B 55 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER D 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE B 57 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 51 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA F 54 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA D 53 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU D 55 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER F 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE D 57 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL F 51 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA H 54 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA F 53 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU F 55 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER H 58 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE F 57 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL H 51 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA J 54 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA H 53 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU H 55 " --> pdb=" O LYS J 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER J 58 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE H 57 " --> pdb=" O SER J 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL J 51 " --> pdb=" O TRP L 52 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA L 54 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA J 53 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS L 56 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU J 55 " --> pdb=" O LYS L 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER L 58 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE J 57 " --> pdb=" O SER L 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 67 200 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1140 1.30 - 1.42: 2280 1.42 - 1.54: 3324 1.54 - 1.66: 12 1.66 - 1.79: 48 Bond restraints: 6804 Sorted by residual: bond pdb=" C ILE D 6 " pdb=" O ILE D 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.91e+01 bond pdb=" C ILE L 6 " pdb=" O ILE L 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.91e+01 bond pdb=" C ILE K 6 " pdb=" O ILE K 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.91e+01 bond pdb=" C ILE H 6 " pdb=" O ILE H 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.90e+01 bond pdb=" C ILE G 6 " pdb=" O ILE G 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.90e+01 ... (remaining 6799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 7353 1.93 - 3.86: 1419 3.86 - 5.79: 264 5.79 - 7.72: 61 7.72 - 9.66: 11 Bond angle restraints: 9108 Sorted by residual: angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.46 120.12 -9.66 1.43e+00 4.89e-01 4.56e+01 angle pdb=" N GLY B 49 " pdb=" CA GLY B 49 " pdb=" C GLY B 49 " ideal model delta sigma weight residual 110.46 120.11 -9.65 1.43e+00 4.89e-01 4.55e+01 angle pdb=" N GLY A 49 " pdb=" CA GLY A 49 " pdb=" C GLY A 49 " ideal model delta sigma weight residual 110.46 120.09 -9.63 1.43e+00 4.89e-01 4.54e+01 angle pdb=" N GLY G 49 " pdb=" CA GLY G 49 " pdb=" C GLY G 49 " ideal model delta sigma weight residual 110.46 120.08 -9.62 1.43e+00 4.89e-01 4.52e+01 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 110.46 120.07 -9.61 1.43e+00 4.89e-01 4.52e+01 ... (remaining 9103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.12: 3048 11.12 - 22.25: 384 22.25 - 33.37: 180 33.37 - 44.49: 60 44.49 - 55.62: 36 Dihedral angle restraints: 3708 sinusoidal: 1464 harmonic: 2244 Sorted by residual: dihedral pdb=" CA SER K 58 " pdb=" C SER K 58 " pdb=" N ASP K 59 " pdb=" CA ASP K 59 " ideal model delta harmonic sigma weight residual 180.00 166.03 13.97 0 5.00e+00 4.00e-02 7.80e+00 dihedral pdb=" CA SER L 58 " pdb=" C SER L 58 " pdb=" N ASP L 59 " pdb=" CA ASP L 59 " ideal model delta harmonic sigma weight residual 180.00 166.07 13.93 0 5.00e+00 4.00e-02 7.77e+00 dihedral pdb=" CA SER A 58 " pdb=" C SER A 58 " pdb=" N ASP A 59 " pdb=" CA ASP A 59 " ideal model delta harmonic sigma weight residual 180.00 166.09 13.91 0 5.00e+00 4.00e-02 7.74e+00 ... (remaining 3705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 349 0.056 - 0.111: 191 0.111 - 0.167: 108 0.167 - 0.222: 84 0.222 - 0.278: 12 Chirality restraints: 744 Sorted by residual: chirality pdb=" CA ALA A 9 " pdb=" N ALA A 9 " pdb=" C ALA A 9 " pdb=" CB ALA A 9 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ALA E 9 " pdb=" N ALA E 9 " pdb=" C ALA E 9 " pdb=" CB ALA E 9 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ALA B 9 " pdb=" N ALA B 9 " pdb=" C ALA B 9 " pdb=" CB ALA B 9 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 741 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 45 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLN K 45 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN K 45 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG K 46 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 45 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLN B 45 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN B 45 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG B 46 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 45 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C GLN I 45 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN I 45 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG I 46 " 0.020 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 3855 3.02 - 3.49: 5880 3.49 - 3.96: 11333 3.96 - 4.43: 13888 4.43 - 4.90: 25547 Nonbonded interactions: 60503 Sorted by model distance: nonbonded pdb=" O ASP L 22 " pdb=" OD1 ASP L 22 " model vdw 2.550 3.040 nonbonded pdb=" O ASP J 22 " pdb=" OD1 ASP J 22 " model vdw 2.550 3.040 nonbonded pdb=" O ASP H 22 " pdb=" OD1 ASP H 22 " model vdw 2.551 3.040 nonbonded pdb=" O ASP D 22 " pdb=" OD1 ASP D 22 " model vdw 2.551 3.040 nonbonded pdb=" O ASP F 22 " pdb=" OD1 ASP F 22 " model vdw 2.551 3.040 ... (remaining 60498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.017 0.060 6804 Z= 1.182 Angle : 1.671 9.655 9108 Z= 1.121 Chirality : 0.100 0.278 744 Planarity : 0.008 0.040 1236 Dihedral : 13.711 55.616 2316 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -3.46 (0.17), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.13), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 46 TYR 0.043 0.007 TYR D 20 PHE 0.028 0.002 PHE F 2 TRP 0.020 0.004 TRP L 17 HIS 0.001 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.01735 ( 6804) covalent geometry : angle 1.67127 ( 9108) hydrogen bonds : bond 0.29924 ( 200) hydrogen bonds : angle 10.38876 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.241 Fit side-chains REVERT: A 65 GLN cc_start: 0.9123 (mt0) cc_final: 0.8892 (mt0) REVERT: B 38 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7415 (tpp80) REVERT: B 45 GLN cc_start: 0.8993 (mt0) cc_final: 0.8779 (mt0) REVERT: B 56 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8275 (mttt) REVERT: B 65 GLN cc_start: 0.9030 (mt0) cc_final: 0.8772 (mt0) REVERT: C 22 ASP cc_start: 0.7977 (t0) cc_final: 0.7695 (t0) REVERT: C 38 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7254 (tpp-160) REVERT: C 65 GLN cc_start: 0.9045 (mt0) cc_final: 0.8822 (mt0) REVERT: D 25 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7811 (mp0) REVERT: D 38 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7252 (ttt90) REVERT: D 45 GLN cc_start: 0.9012 (mt0) cc_final: 0.8774 (mt0) REVERT: E 38 ARG cc_start: 0.7575 (ttt180) cc_final: 0.7168 (tpp80) REVERT: F 16 MET cc_start: 0.9173 (mtt) cc_final: 0.8971 (mtt) REVERT: F 25 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7942 (mt-10) REVERT: F 38 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7027 (tpp80) REVERT: F 66 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8593 (mt-10) REVERT: G 22 ASP cc_start: 0.7943 (t0) cc_final: 0.7161 (t0) REVERT: G 25 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8123 (mp0) REVERT: G 38 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7081 (tpp80) REVERT: H 25 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7740 (mp0) REVERT: H 38 ARG cc_start: 0.7526 (ttt180) cc_final: 0.7096 (tpp80) REVERT: I 22 ASP cc_start: 0.7958 (t0) cc_final: 0.7738 (t0) REVERT: I 25 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 38 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7458 (tpp-160) REVERT: I 56 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8115 (mttp) REVERT: I 66 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8536 (mt-10) REVERT: J 16 MET cc_start: 0.9156 (mtt) cc_final: 0.8941 (mtt) REVERT: J 22 ASP cc_start: 0.7976 (t0) cc_final: 0.7461 (t0) REVERT: J 23 MET cc_start: 0.8768 (mtt) cc_final: 0.8469 (mtt) REVERT: J 25 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7463 (mt-10) REVERT: J 38 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7261 (ttt90) REVERT: J 65 GLN cc_start: 0.9189 (mt0) cc_final: 0.8984 (mt0) REVERT: K 63 SER cc_start: 0.8847 (m) cc_final: 0.8526 (p) REVERT: K 66 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8585 (mt-10) REVERT: L 8 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7538 (mp0) REVERT: L 25 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8157 (mp0) REVERT: L 29 LYS cc_start: 0.8468 (tttp) cc_final: 0.8172 (tttp) REVERT: L 38 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7621 (ttt180) REVERT: L 46 ARG cc_start: 0.8376 (tpt90) cc_final: 0.5820 (mpt180) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.7687 time to fit residues: 168.4399 Evaluate side-chains 202 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.123728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101905 restraints weight = 7967.355| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.52 r_work: 0.3488 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6804 Z= 0.136 Angle : 0.533 4.521 9108 Z= 0.334 Chirality : 0.043 0.124 744 Planarity : 0.004 0.038 1236 Dihedral : 4.352 15.762 900 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.60 % Allowed : 16.32 % Favored : 81.08 % 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: -3.73 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.006 0.001 TYR G 20 PHE 0.014 0.001 PHE E 2 TRP 0.007 0.001 TRP G 28 HIS 0.001 0.000 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6804) covalent geometry : angle 0.53330 ( 9108) hydrogen bonds : bond 0.05632 ( 200) hydrogen bonds : angle 6.51822 ( 600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: B 38 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8195 (tpp80) REVERT: C 38 ARG cc_start: 0.8312 (ttt180) cc_final: 0.8072 (tpp-160) REVERT: C 65 GLN cc_start: 0.9070 (mt0) cc_final: 0.8833 (mt0) REVERT: D 38 ARG cc_start: 0.8267 (ttt180) cc_final: 0.8043 (ttt90) REVERT: E 25 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8475 (mp0) REVERT: E 29 LYS cc_start: 0.8627 (tttt) cc_final: 0.7863 (tptt) REVERT: E 38 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7957 (tpp80) REVERT: F 38 ARG cc_start: 0.8258 (ttt180) cc_final: 0.7849 (tpp80) REVERT: G 38 ARG cc_start: 0.8172 (ttt180) cc_final: 0.7789 (tpp80) REVERT: H 38 ARG cc_start: 0.8177 (ttt180) cc_final: 0.7554 (tpp80) REVERT: H 46 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8392 (tmt170) REVERT: I 25 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8626 (mt-10) REVERT: I 38 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8167 (tpp-160) REVERT: I 56 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8355 (mttp) REVERT: I 62 GLU cc_start: 0.8064 (tp30) cc_final: 0.7789 (tp30) REVERT: J 25 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8269 (mt-10) REVERT: J 38 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7907 (tpp-160) REVERT: J 65 GLN cc_start: 0.9206 (mt0) cc_final: 0.8882 (mt0) REVERT: K 25 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8553 (mt-10) REVERT: K 38 ARG cc_start: 0.8428 (ttt180) cc_final: 0.7769 (tpp80) REVERT: K 63 SER cc_start: 0.9031 (m) cc_final: 0.8801 (p) REVERT: L 8 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8010 (mt-10) REVERT: L 46 ARG cc_start: 0.8537 (tpt90) cc_final: 0.5980 (mpt-90) outliers start: 15 outliers final: 3 residues processed: 165 average time/residue: 0.8367 time to fit residues: 142.2674 Evaluate side-chains 159 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain L residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 45 GLN C 45 GLN D 45 GLN D 65 GLN E 45 GLN F 45 GLN H 45 GLN L 65 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.117313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.095065 restraints weight = 7948.836| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.51 r_work: 0.3393 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6804 Z= 0.331 Angle : 0.598 5.225 9108 Z= 0.365 Chirality : 0.045 0.130 744 Planarity : 0.003 0.034 1236 Dihedral : 4.876 20.240 900 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.56 % Allowed : 17.36 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.80 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.13), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 18 TYR 0.010 0.002 TYR A 20 PHE 0.015 0.002 PHE I 2 TRP 0.012 0.002 TRP J 28 HIS 0.001 0.000 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00746 ( 6804) covalent geometry : angle 0.59758 ( 9108) hydrogen bonds : bond 0.06431 ( 200) hydrogen bonds : angle 6.39211 ( 600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: A 32 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: B 65 GLN cc_start: 0.9121 (mt0) cc_final: 0.8892 (mt0) REVERT: C 23 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7935 (mtm) REVERT: C 65 GLN cc_start: 0.9084 (mt0) cc_final: 0.8851 (mt0) REVERT: D 25 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8090 (mp0) REVERT: D 38 ARG cc_start: 0.8288 (ttt180) cc_final: 0.7979 (ttt90) REVERT: E 38 ARG cc_start: 0.8278 (ttt180) cc_final: 0.7984 (tpp80) REVERT: F 38 ARG cc_start: 0.8260 (ttt180) cc_final: 0.8025 (tpp80) REVERT: G 8 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8439 (mt-10) REVERT: G 38 ARG cc_start: 0.8201 (ttt180) cc_final: 0.7795 (tpp80) REVERT: G 66 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8716 (mt-10) REVERT: H 23 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: H 25 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8262 (mp0) REVERT: H 38 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7890 (ttt180) REVERT: I 25 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8544 (mt-10) REVERT: I 38 ARG cc_start: 0.8489 (ttt180) cc_final: 0.8265 (tpp-160) REVERT: I 56 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8339 (mttp) REVERT: J 25 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8456 (mt-10) REVERT: J 65 GLN cc_start: 0.9227 (mt0) cc_final: 0.8906 (mt0) REVERT: K 32 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: L 8 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8202 (mt-10) REVERT: L 29 LYS cc_start: 0.8371 (tttp) cc_final: 0.8170 (tttp) REVERT: L 46 ARG cc_start: 0.8651 (tpt90) cc_final: 0.5982 (mpt180) outliers start: 32 outliers final: 8 residues processed: 165 average time/residue: 0.8130 time to fit residues: 138.2658 Evaluate side-chains 170 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096794 restraints weight = 7963.568| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.57 r_work: 0.3430 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6804 Z= 0.212 Angle : 0.531 4.878 9108 Z= 0.325 Chirality : 0.043 0.128 744 Planarity : 0.003 0.034 1236 Dihedral : 4.744 19.357 900 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.69 % Allowed : 17.88 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.85 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.008 0.001 TYR L 34 PHE 0.013 0.002 PHE I 2 TRP 0.011 0.001 TRP J 28 HIS 0.001 0.000 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6804) covalent geometry : angle 0.53060 ( 9108) hydrogen bonds : bond 0.05346 ( 200) hydrogen bonds : angle 6.20607 ( 600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: B 65 GLN cc_start: 0.9137 (mt0) cc_final: 0.8891 (mt0) REVERT: C 65 GLN cc_start: 0.9081 (mt0) cc_final: 0.8872 (mt0) REVERT: D 25 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8101 (mp0) REVERT: D 38 ARG cc_start: 0.8288 (ttt180) cc_final: 0.7816 (ttm-80) REVERT: E 29 LYS cc_start: 0.8618 (tttt) cc_final: 0.7831 (tptt) REVERT: E 38 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7929 (tpp80) REVERT: G 8 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: G 25 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8146 (mp0) REVERT: G 38 ARG cc_start: 0.8197 (ttt180) cc_final: 0.7785 (tpp80) REVERT: G 46 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.6941 (tmt170) REVERT: G 66 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8716 (mt-10) REVERT: H 25 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8205 (mp0) REVERT: H 38 ARG cc_start: 0.8148 (ttt180) cc_final: 0.7526 (tpp80) REVERT: I 25 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8480 (mt-10) REVERT: I 38 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8264 (tpp-160) REVERT: I 62 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: J 25 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8381 (mt-10) REVERT: J 65 GLN cc_start: 0.9242 (mt0) cc_final: 0.8980 (mt0) REVERT: K 25 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8547 (mt-10) REVERT: L 8 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8126 (mt-10) REVERT: L 46 ARG cc_start: 0.8660 (tpt90) cc_final: 0.5964 (mpt180) outliers start: 27 outliers final: 4 residues processed: 164 average time/residue: 0.8131 time to fit residues: 137.5726 Evaluate side-chains 164 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.120898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.098067 restraints weight = 7983.400| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.59 r_work: 0.3454 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6804 Z= 0.168 Angle : 0.504 4.633 9108 Z= 0.308 Chirality : 0.042 0.126 744 Planarity : 0.002 0.028 1236 Dihedral : 4.622 18.696 900 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.17 % Allowed : 18.75 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.83 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.007 0.001 TYR L 34 PHE 0.011 0.001 PHE I 2 TRP 0.012 0.001 TRP G 28 HIS 0.001 0.000 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6804) covalent geometry : angle 0.50383 ( 9108) hydrogen bonds : bond 0.04786 ( 200) hydrogen bonds : angle 6.09092 ( 600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 46 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8391 (tmt170) REVERT: B 65 GLN cc_start: 0.9096 (mt0) cc_final: 0.8853 (mt0) REVERT: C 65 GLN cc_start: 0.9073 (mt0) cc_final: 0.8857 (mt0) REVERT: D 25 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8124 (mp0) REVERT: D 38 ARG cc_start: 0.8262 (ttt180) cc_final: 0.7814 (ttm-80) REVERT: E 25 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8527 (mp0) REVERT: E 29 LYS cc_start: 0.8584 (tttt) cc_final: 0.7775 (tptt) REVERT: E 38 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7936 (tpp80) REVERT: G 8 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: G 25 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8191 (mp0) REVERT: G 38 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7769 (tpp80) REVERT: G 46 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7011 (tmt170) REVERT: G 66 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8686 (mt-10) REVERT: H 25 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8206 (mp0) REVERT: H 38 ARG cc_start: 0.8157 (ttt180) cc_final: 0.7582 (tpp80) REVERT: I 25 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8485 (mt-10) REVERT: I 38 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8265 (tpp-160) REVERT: I 62 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: J 25 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8462 (mt-10) REVERT: J 65 GLN cc_start: 0.9222 (mt0) cc_final: 0.8970 (mt0) REVERT: K 25 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8547 (mt-10) REVERT: L 8 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8116 (mt-10) REVERT: L 46 ARG cc_start: 0.8677 (tpt90) cc_final: 0.5968 (mpt180) outliers start: 24 outliers final: 5 residues processed: 162 average time/residue: 0.8143 time to fit residues: 136.0564 Evaluate side-chains 165 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN L 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.121198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098295 restraints weight = 7952.117| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.59 r_work: 0.3467 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6804 Z= 0.155 Angle : 0.494 4.584 9108 Z= 0.302 Chirality : 0.042 0.129 744 Planarity : 0.002 0.028 1236 Dihedral : 4.541 18.221 900 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.34 % Allowed : 20.14 % Favored : 75.52 % 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: -3.79 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.004 0.001 TYR A 20 PHE 0.010 0.001 PHE I 2 TRP 0.012 0.001 TRP G 28 HIS 0.001 0.000 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6804) covalent geometry : angle 0.49386 ( 9108) hydrogen bonds : bond 0.04557 ( 200) hydrogen bonds : angle 6.00499 ( 600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: A 32 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: A 46 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8380 (tmt170) REVERT: B 65 GLN cc_start: 0.9106 (mt0) cc_final: 0.8856 (mt0) REVERT: C 65 GLN cc_start: 0.9080 (mt0) cc_final: 0.8859 (mt0) REVERT: D 25 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8117 (mp0) REVERT: D 38 ARG cc_start: 0.8312 (ttt180) cc_final: 0.7898 (ttm-80) REVERT: E 25 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8510 (mp0) REVERT: E 29 LYS cc_start: 0.8559 (tttt) cc_final: 0.7733 (tptt) REVERT: E 38 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7910 (tpp80) REVERT: G 8 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: G 25 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8198 (mp0) REVERT: G 38 ARG cc_start: 0.8148 (ttt180) cc_final: 0.7733 (tpp80) REVERT: G 46 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.6984 (tmt170) REVERT: G 66 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: H 25 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8455 (mp0) REVERT: H 38 ARG cc_start: 0.8189 (ttt180) cc_final: 0.7613 (tpp80) REVERT: I 25 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8508 (mt-10) REVERT: I 38 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8266 (tpp-160) REVERT: I 62 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: J 25 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8574 (mt-10) REVERT: J 65 GLN cc_start: 0.9210 (mt0) cc_final: 0.8955 (mt0) REVERT: K 23 MET cc_start: 0.9091 (mtt) cc_final: 0.8714 (mtt) REVERT: K 25 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8534 (mt-10) REVERT: L 8 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8223 (mt-10) REVERT: L 46 ARG cc_start: 0.8679 (tpt90) cc_final: 0.5924 (mpt180) outliers start: 25 outliers final: 7 residues processed: 164 average time/residue: 0.8095 time to fit residues: 136.9038 Evaluate side-chains 165 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 45 GLN D 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.119087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096329 restraints weight = 7934.101| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.57 r_work: 0.3429 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6804 Z= 0.225 Angle : 0.526 4.793 9108 Z= 0.320 Chirality : 0.043 0.128 744 Planarity : 0.004 0.098 1236 Dihedral : 4.745 19.631 900 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.34 % Allowed : 20.14 % Favored : 75.52 % 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: -3.83 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 18 TYR 0.012 0.001 TYR I 34 PHE 0.011 0.002 PHE D 2 TRP 0.013 0.002 TRP J 28 HIS 0.001 0.000 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 6804) covalent geometry : angle 0.52577 ( 9108) hydrogen bonds : bond 0.05150 ( 200) hydrogen bonds : angle 6.05439 ( 600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: A 32 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: A 46 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8394 (tmt170) REVERT: B 65 GLN cc_start: 0.9081 (mt0) cc_final: 0.8835 (mt0) REVERT: C 65 GLN cc_start: 0.9092 (mt0) cc_final: 0.8868 (mt0) REVERT: D 25 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8093 (mp0) REVERT: D 38 ARG cc_start: 0.8272 (ttt180) cc_final: 0.7789 (ttt90) REVERT: E 25 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8517 (mp0) REVERT: E 29 LYS cc_start: 0.8596 (tttt) cc_final: 0.7722 (tptt) REVERT: E 38 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7901 (tpp80) REVERT: G 8 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: G 25 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8231 (mp0) REVERT: G 38 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7840 (tpp80) REVERT: G 46 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.6994 (tmt170) REVERT: G 66 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8688 (mt-10) REVERT: H 25 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8429 (mp0) REVERT: H 38 ARG cc_start: 0.8151 (ttt180) cc_final: 0.7935 (tpp-160) REVERT: I 25 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8541 (mt-10) REVERT: I 38 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8260 (tpp-160) REVERT: I 62 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: J 25 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8550 (mt-10) REVERT: J 65 GLN cc_start: 0.9228 (mt0) cc_final: 0.8994 (mt0) REVERT: K 25 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8518 (mt-10) REVERT: L 8 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8135 (mt-10) REVERT: L 29 LYS cc_start: 0.8197 (tttp) cc_final: 0.7955 (tttp) REVERT: L 46 ARG cc_start: 0.8676 (tpt90) cc_final: 0.5955 (mpt180) outliers start: 25 outliers final: 10 residues processed: 159 average time/residue: 0.7915 time to fit residues: 129.8668 Evaluate side-chains 168 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.119300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096430 restraints weight = 7994.201| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.59 r_work: 0.3437 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6804 Z= 0.207 Angle : 0.520 4.752 9108 Z= 0.316 Chirality : 0.043 0.127 744 Planarity : 0.003 0.086 1236 Dihedral : 4.704 19.491 900 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.51 % Allowed : 20.49 % Favored : 75.00 % 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: -3.84 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.010 0.001 TYR J 34 PHE 0.011 0.001 PHE D 2 TRP 0.013 0.002 TRP J 28 HIS 0.001 0.000 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6804) covalent geometry : angle 0.51981 ( 9108) hydrogen bonds : bond 0.04972 ( 200) hydrogen bonds : angle 6.02987 ( 600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: A 32 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: A 46 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8311 (tmt170) REVERT: B 65 GLN cc_start: 0.9078 (mt0) cc_final: 0.8828 (mt0) REVERT: C 65 GLN cc_start: 0.9087 (mt0) cc_final: 0.8860 (mt0) REVERT: D 25 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8121 (mp0) REVERT: D 38 ARG cc_start: 0.8316 (ttt180) cc_final: 0.7837 (ttt90) REVERT: D 66 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8839 (mt-10) REVERT: E 25 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8530 (mp0) REVERT: E 29 LYS cc_start: 0.8594 (tttt) cc_final: 0.7716 (tptt) REVERT: E 38 ARG cc_start: 0.8234 (ttt180) cc_final: 0.7917 (tpp80) REVERT: G 8 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: G 25 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8272 (mp0) REVERT: G 38 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7844 (tpp80) REVERT: G 46 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.6989 (tmt170) REVERT: G 66 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8680 (mt-10) REVERT: H 25 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8462 (mp0) REVERT: H 38 ARG cc_start: 0.8154 (ttt180) cc_final: 0.7942 (tpp-160) REVERT: I 25 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8606 (mt-10) REVERT: I 38 ARG cc_start: 0.8467 (ttt180) cc_final: 0.8251 (tpp-160) REVERT: I 62 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: J 25 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8576 (mt-10) REVERT: J 65 GLN cc_start: 0.9229 (mt0) cc_final: 0.8997 (mt0) REVERT: K 25 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8522 (mt-10) REVERT: L 8 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8120 (mt-10) REVERT: L 46 ARG cc_start: 0.8712 (tpt90) cc_final: 0.5977 (mpt180) outliers start: 26 outliers final: 13 residues processed: 159 average time/residue: 0.7796 time to fit residues: 127.9537 Evaluate side-chains 169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.120301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.097361 restraints weight = 7983.978| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.59 r_work: 0.3453 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6804 Z= 0.184 Angle : 0.512 4.634 9108 Z= 0.311 Chirality : 0.043 0.126 744 Planarity : 0.003 0.086 1236 Dihedral : 4.640 19.193 900 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.69 % Allowed : 20.49 % Favored : 74.83 % 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: -3.86 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.010 0.001 TYR J 34 PHE 0.011 0.001 PHE D 2 TRP 0.015 0.001 TRP I 28 HIS 0.001 0.000 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6804) covalent geometry : angle 0.51183 ( 9108) hydrogen bonds : bond 0.04757 ( 200) hydrogen bonds : angle 5.98763 ( 600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: A 32 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: A 46 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8386 (tmt170) REVERT: B 65 GLN cc_start: 0.9075 (mt0) cc_final: 0.8822 (mt0) REVERT: C 65 GLN cc_start: 0.9087 (mt0) cc_final: 0.8856 (mt0) REVERT: D 25 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8118 (mp0) REVERT: D 38 ARG cc_start: 0.8309 (ttt180) cc_final: 0.7826 (ttt90) REVERT: E 25 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8506 (mp0) REVERT: E 29 LYS cc_start: 0.8596 (tttt) cc_final: 0.7722 (tptt) REVERT: E 38 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7925 (tpp80) REVERT: G 8 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: G 25 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8276 (mp0) REVERT: G 38 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7835 (tpp80) REVERT: G 46 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.6967 (tmt170) REVERT: G 66 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: H 25 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8483 (mp0) REVERT: I 25 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8610 (mt-10) REVERT: I 38 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8245 (tpp-160) REVERT: I 62 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: J 18 ARG cc_start: 0.8828 (ptp-170) cc_final: 0.8499 (pmm-80) REVERT: J 25 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8531 (mt-10) REVERT: J 38 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7079 (ttp-170) REVERT: J 65 GLN cc_start: 0.9230 (mt0) cc_final: 0.8997 (mt0) REVERT: K 25 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8484 (mt-10) REVERT: L 8 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8105 (mt-10) REVERT: L 46 ARG cc_start: 0.8718 (tpt90) cc_final: 0.5979 (mpt180) outliers start: 27 outliers final: 12 residues processed: 163 average time/residue: 0.8231 time to fit residues: 138.3145 Evaluate side-chains 173 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.117164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094421 restraints weight = 8043.332| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.57 r_work: 0.3402 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 6804 Z= 0.317 Angle : 0.581 5.181 9108 Z= 0.350 Chirality : 0.045 0.131 744 Planarity : 0.004 0.104 1236 Dihedral : 4.967 20.622 900 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.34 % Allowed : 21.18 % Favored : 74.48 % 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: -3.93 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 18 TYR 0.011 0.001 TYR J 34 PHE 0.014 0.002 PHE A 5 TRP 0.022 0.002 TRP I 28 HIS 0.001 0.000 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00717 ( 6804) covalent geometry : angle 0.58112 ( 9108) hydrogen bonds : bond 0.05722 ( 200) hydrogen bonds : angle 6.11159 ( 600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 32 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: A 46 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8323 (tmt170) REVERT: B 65 GLN cc_start: 0.9079 (mt0) cc_final: 0.8834 (mt0) REVERT: C 65 GLN cc_start: 0.9105 (mt0) cc_final: 0.8876 (mt0) REVERT: D 25 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8070 (mp0) REVERT: D 38 ARG cc_start: 0.8255 (ttt180) cc_final: 0.7779 (ttt90) REVERT: E 38 ARG cc_start: 0.8260 (ttt180) cc_final: 0.7947 (tpp80) REVERT: G 8 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: G 25 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8269 (mp0) REVERT: G 38 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7856 (tpp80) REVERT: G 46 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.6988 (tmt170) REVERT: G 66 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: H 8 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: H 25 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8449 (mp0) REVERT: I 25 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8608 (mt-10) REVERT: I 38 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8262 (tpp-160) REVERT: J 25 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8630 (mt-10) REVERT: J 65 GLN cc_start: 0.9258 (mt0) cc_final: 0.8916 (mt0) REVERT: K 25 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8479 (mt-10) REVERT: L 8 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8157 (mt-10) REVERT: L 46 ARG cc_start: 0.8708 (tpt90) cc_final: 0.5974 (mpt180) outliers start: 25 outliers final: 12 residues processed: 161 average time/residue: 0.8146 time to fit residues: 135.2737 Evaluate side-chains 174 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 0.0270 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 GLN F 45 GLN H 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.125010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102540 restraints weight = 7673.652| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.44 r_work: 0.3519 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6804 Z= 0.103 Angle : 0.486 4.623 9108 Z= 0.294 Chirality : 0.041 0.125 744 Planarity : 0.003 0.074 1236 Dihedral : 4.364 18.424 900 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.91 % Allowed : 23.96 % Favored : 74.13 % 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: -3.84 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.011 0.001 TYR J 34 PHE 0.011 0.001 PHE E 2 TRP 0.017 0.001 TRP I 28 HIS 0.000 0.000 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6804) covalent geometry : angle 0.48590 ( 9108) hydrogen bonds : bond 0.03846 ( 200) hydrogen bonds : angle 5.90212 ( 600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.29 seconds wall clock time: 57 minutes 36.06 seconds (3456.06 seconds total)