Starting phenix.real_space_refine on Tue Feb 3 22:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hc6_52038/02_2026/9hc6_52038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hc6_52038/02_2026/9hc6_52038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hc6_52038/02_2026/9hc6_52038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hc6_52038/02_2026/9hc6_52038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hc6_52038/02_2026/9hc6_52038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hc6_52038/02_2026/9hc6_52038.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4740 2.51 5 N 1305 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7560 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 504 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 0.64, per 1000 atoms: 0.08 Number of scatterers: 7560 At special positions: 0 Unit cell: (145.95, 139.65, 43.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1515 8.00 N 1305 7.00 C 4740 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: 0.65 Conformation dependent library (CDL) restraints added in 369.5 milliseconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.615A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA C 19 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LYS C 21 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU B 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ALA D 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA C 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LYS D 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU C 20 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 5.978A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 49 removed outlier: 6.797A pdb=" N TYR B 39 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 40 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY B 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 42 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS B 43 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 44 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS B 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR C 39 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 40 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY C 41 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 42 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS C 43 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS C 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR D 39 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 40 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 41 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER C 42 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS D 43 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR C 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS D 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR E 39 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 40 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY E 41 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER D 42 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS E 43 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR D 44 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS E 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 79 removed outlier: 8.806A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY B 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR A 72 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR B 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN B 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N GLY C 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL C 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N GLY D 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR C 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N THR D 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL D 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY E 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR D 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR E 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL D 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL E 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN E 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 95 Processing sheet with id=AA8, first strand: chain 'F' and resid 16 through 22 removed outlier: 6.614A pdb=" N VAL F 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA G 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA F 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS G 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU F 20 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA H 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL H 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA I 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA H 18 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU H 20 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL I 16 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA J 19 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA I 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS J 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU I 20 " --> pdb=" O LYS J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 34 through 35 removed outlier: 5.978A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 38 through 49 removed outlier: 6.797A pdb=" N TYR G 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL F 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY G 41 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER F 42 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS G 43 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR F 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS G 45 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR H 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 40 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY H 41 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER G 42 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS H 43 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR G 44 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS H 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR I 39 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL H 40 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY I 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER H 42 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS I 43 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR H 44 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS I 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR J 39 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL I 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY J 41 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER I 42 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS J 43 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR I 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS J 45 " --> pdb=" O THR I 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 52 through 57 Processing sheet with id=AB3, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 79 removed outlier: 8.806A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY G 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR F 72 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N THR G 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL F 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL G 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN G 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA F 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY H 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR G 72 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR H 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN H 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA G 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY I 73 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR H 72 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR I 75 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL H 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL I 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN I 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA H 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY J 73 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR I 72 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N THR J 75 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL I 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL J 77 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN J 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA I 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 86 through 95 Processing sheet with id=AB6, first strand: chain 'K' and resid 16 through 22 removed outlier: 6.615A pdb=" N VAL K 16 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA L 19 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA K 18 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS L 21 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU K 20 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL L 16 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA M 19 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA L 18 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS M 21 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU L 20 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL M 16 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA N 19 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA M 18 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LYS N 21 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU M 20 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL N 16 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA O 19 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA N 18 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS O 21 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU N 20 " --> pdb=" O LYS O 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 34 through 35 removed outlier: 5.979A pdb=" N LYS K 34 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS L 34 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS M 34 " --> pdb=" O GLU N 35 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS N 34 " --> pdb=" O GLU O 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 38 through 49 removed outlier: 6.797A pdb=" N TYR L 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL K 40 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY L 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER K 42 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS L 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR K 44 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS L 45 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR M 39 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL L 40 " --> pdb=" O TYR M 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY M 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER L 42 " --> pdb=" O GLY M 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS M 43 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR L 44 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS M 45 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR N 39 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL M 40 " --> pdb=" O TYR N 39 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY N 41 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER M 42 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS N 43 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR M 44 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS N 45 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR O 39 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL N 40 " --> pdb=" O TYR O 39 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY O 41 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER N 42 " --> pdb=" O GLY O 41 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS O 43 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR N 44 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS O 45 " --> pdb=" O THR N 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 52 through 57 Processing sheet with id=AC1, first strand: chain 'K' and resid 61 through 66 Processing sheet with id=AC2, first strand: chain 'K' and resid 70 through 79 removed outlier: 8.806A pdb=" N VAL K 70 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY L 73 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR K 72 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N THR L 75 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL K 74 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL L 77 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA K 76 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN L 79 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA K 78 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL L 70 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N GLY M 73 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR L 72 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR M 75 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL L 74 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL M 77 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA L 76 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN M 79 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA L 78 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL M 70 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N GLY N 73 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR M 72 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N THR N 75 " --> pdb=" O THR M 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL M 74 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL N 77 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA M 76 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN N 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA M 78 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL N 70 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLY O 73 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N THR N 72 " --> pdb=" O GLY O 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR O 75 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL N 74 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL O 77 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA N 76 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN O 79 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA N 78 " --> pdb=" O GLN O 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 86 through 95 276 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 1320 1.26 - 1.33: 1114 1.33 - 1.41: 266 1.41 - 1.48: 1305 1.48 - 1.55: 3570 Bond restraints: 7575 Sorted by residual: bond pdb=" C GLY G 73 " pdb=" O GLY G 73 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.12e-02 7.97e+03 1.73e+01 bond pdb=" C GLY N 73 " pdb=" O GLY N 73 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.12e-02 7.97e+03 1.72e+01 bond pdb=" C GLY M 73 " pdb=" O GLY M 73 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.12e-02 7.97e+03 1.72e+01 bond pdb=" C GLY I 73 " pdb=" O GLY I 73 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.12e-02 7.97e+03 1.72e+01 bond pdb=" C GLY H 73 " pdb=" O GLY H 73 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.12e-02 7.97e+03 1.71e+01 ... (remaining 7570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 7746 1.96 - 3.93: 1915 3.93 - 5.89: 376 5.89 - 7.86: 118 7.86 - 9.82: 60 Bond angle restraints: 10215 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 110.62 100.80 9.82 1.02e+00 9.61e-01 9.27e+01 angle pdb=" N VAL I 74 " pdb=" CA VAL I 74 " pdb=" C VAL I 74 " ideal model delta sigma weight residual 110.62 100.81 9.81 1.02e+00 9.61e-01 9.24e+01 angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 110.62 100.82 9.80 1.02e+00 9.61e-01 9.24e+01 angle pdb=" N VAL O 74 " pdb=" CA VAL O 74 " pdb=" C VAL O 74 " ideal model delta sigma weight residual 110.62 100.82 9.80 1.02e+00 9.61e-01 9.23e+01 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 110.62 100.83 9.79 1.02e+00 9.61e-01 9.22e+01 ... (remaining 10210 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.10: 3825 17.10 - 34.20: 360 34.20 - 51.29: 195 51.29 - 68.38: 75 68.38 - 85.48: 15 Dihedral angle restraints: 4470 sinusoidal: 1500 harmonic: 2970 Sorted by residual: dihedral pdb=" C HIS D 50 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " pdb=" CB HIS D 50 " ideal model delta harmonic sigma weight residual -122.60 -132.30 9.70 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" C HIS O 50 " pdb=" N HIS O 50 " pdb=" CA HIS O 50 " pdb=" CB HIS O 50 " ideal model delta harmonic sigma weight residual -122.60 -132.30 9.70 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" C HIS I 50 " pdb=" N HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta harmonic sigma weight residual -122.60 -132.28 9.68 0 2.50e+00 1.60e-01 1.50e+01 ... (remaining 4467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1037 0.098 - 0.196: 283 0.196 - 0.294: 30 0.294 - 0.391: 0 0.391 - 0.489: 15 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA HIS D 50 " pdb=" N HIS D 50 " pdb=" C HIS D 50 " pdb=" CB HIS D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA HIS C 50 " pdb=" N HIS C 50 " pdb=" C HIS C 50 " pdb=" CB HIS C 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA HIS I 50 " pdb=" N HIS I 50 " pdb=" C HIS I 50 " pdb=" CB HIS I 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 1362 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 72 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C THR G 72 " -0.039 2.00e-02 2.50e+03 pdb=" O THR G 72 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY G 73 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR K 72 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C THR K 72 " -0.038 2.00e-02 2.50e+03 pdb=" O THR K 72 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY K 73 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 72 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C THR F 72 " -0.038 2.00e-02 2.50e+03 pdb=" O THR F 72 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY F 73 " 0.013 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 3725 2.97 - 3.45: 6793 3.45 - 3.93: 13267 3.93 - 4.42: 15389 4.42 - 4.90: 26768 Nonbonded interactions: 65942 Sorted by model distance: nonbonded pdb=" CG1 VAL I 82 " pdb=" O GLY I 84 " model vdw 2.484 3.460 nonbonded pdb=" CG1 VAL N 82 " pdb=" O GLY N 84 " model vdw 2.484 3.460 nonbonded pdb=" CG1 VAL E 82 " pdb=" O GLY E 84 " model vdw 2.484 3.460 nonbonded pdb=" CG1 VAL K 82 " pdb=" O GLY K 84 " model vdw 2.484 3.460 nonbonded pdb=" CG1 VAL F 82 " pdb=" O GLY F 84 " model vdw 2.484 3.460 ... (remaining 65937 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: 0.03 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.060 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.070 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.014 0.047 7575 Z= 1.114 Angle : 2.025 9.819 10215 Z= 1.402 Chirality : 0.094 0.489 1365 Planarity : 0.005 0.022 1245 Dihedral : 19.707 85.476 2580 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 27.45 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.10 (0.22), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR J 39 PHE 0.026 0.007 PHE G 94 HIS 0.008 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.01442 ( 7575) covalent geometry : angle 2.02523 (10215) hydrogen bonds : bond 0.11912 ( 276) hydrogen bonds : angle 8.07379 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 64 THR cc_start: 0.9031 (m) cc_final: 0.8820 (m) REVERT: C 34 LYS cc_start: 0.8048 (mttt) cc_final: 0.7780 (mtpt) REVERT: D 44 THR cc_start: 0.9105 (t) cc_final: 0.8863 (t) REVERT: D 80 LYS cc_start: 0.9171 (mttp) cc_final: 0.8960 (mttm) REVERT: E 57 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7541 (tm-30) REVERT: E 58 LYS cc_start: 0.8921 (mttt) cc_final: 0.8552 (mtmt) REVERT: F 34 LYS cc_start: 0.7901 (mttt) cc_final: 0.7566 (mtpt) REVERT: G 80 LYS cc_start: 0.9222 (mttp) cc_final: 0.8959 (mttm) REVERT: I 44 THR cc_start: 0.9138 (t) cc_final: 0.8891 (t) REVERT: J 34 LYS cc_start: 0.8272 (mttt) cc_final: 0.8044 (mtmt) REVERT: K 34 LYS cc_start: 0.7918 (mttt) cc_final: 0.7614 (mttt) REVERT: L 54 THR cc_start: 0.9263 (m) cc_final: 0.9059 (m) REVERT: N 44 THR cc_start: 0.9119 (t) cc_final: 0.8886 (t) REVERT: N 64 THR cc_start: 0.8974 (m) cc_final: 0.8743 (m) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.6657 time to fit residues: 186.7113 Evaluate side-chains 240 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094067 restraints weight = 8793.314| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.16 r_work: 0.3231 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7575 Z= 0.250 Angle : 0.556 6.133 10215 Z= 0.330 Chirality : 0.055 0.175 1365 Planarity : 0.003 0.013 1245 Dihedral : 5.644 22.052 1080 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 7.58 % Allowed : 23.01 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.24), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 39 PHE 0.020 0.004 PHE N 94 HIS 0.007 0.003 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 7575) covalent geometry : angle 0.55577 (10215) hydrogen bonds : bond 0.04207 ( 276) hydrogen bonds : angle 5.96556 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9191 (mttt) cc_final: 0.8975 (mttp) REVERT: A 96 LYS cc_start: 0.7824 (mttt) cc_final: 0.7580 (mttt) REVERT: B 20 GLU cc_start: 0.8395 (mp0) cc_final: 0.8180 (mt-10) REVERT: B 57 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: B 64 THR cc_start: 0.9139 (m) cc_final: 0.8908 (m) REVERT: C 34 LYS cc_start: 0.8268 (mttt) cc_final: 0.7880 (mttt) REVERT: C 57 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: D 57 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: E 57 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: E 58 LYS cc_start: 0.9268 (mttt) cc_final: 0.8975 (mttp) REVERT: F 34 LYS cc_start: 0.8343 (mttt) cc_final: 0.7971 (mttt) REVERT: F 57 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: G 57 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: H 45 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8706 (mtpm) REVERT: I 57 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: J 34 LYS cc_start: 0.8408 (mttt) cc_final: 0.8160 (mttt) REVERT: J 57 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: K 34 LYS cc_start: 0.8429 (mttt) cc_final: 0.8222 (mttt) REVERT: L 21 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.7791 (tmtt) REVERT: L 57 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: M 45 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (mtpt) REVERT: M 57 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: N 57 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: O 57 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8136 (tm-30) outliers start: 58 outliers final: 27 residues processed: 224 average time/residue: 0.5989 time to fit residues: 141.1118 Evaluate side-chains 221 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 overall best weight: 5.0386 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.114718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097467 restraints weight = 8510.026| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.03 r_work: 0.3219 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7575 Z= 0.265 Angle : 0.540 6.053 10215 Z= 0.319 Chirality : 0.054 0.132 1365 Planarity : 0.003 0.011 1245 Dihedral : 5.373 21.495 1080 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 8.10 % Allowed : 24.18 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR M 39 PHE 0.020 0.004 PHE I 94 HIS 0.006 0.002 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 7575) covalent geometry : angle 0.53997 (10215) hydrogen bonds : bond 0.03880 ( 276) hydrogen bonds : angle 5.57402 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: B 64 THR cc_start: 0.9141 (m) cc_final: 0.8914 (m) REVERT: C 34 LYS cc_start: 0.8427 (mttt) cc_final: 0.8105 (mttt) REVERT: C 57 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: D 45 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8738 (ttpp) REVERT: D 57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: E 57 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: F 57 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: G 57 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: H 20 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8149 (mt-10) REVERT: H 45 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8637 (mtpt) REVERT: H 57 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: H 58 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8388 (mttp) REVERT: I 57 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: K 34 LYS cc_start: 0.8568 (mttt) cc_final: 0.8335 (mttt) REVERT: K 57 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: L 21 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7917 (tttt) REVERT: L 57 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: M 20 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8182 (mt-10) REVERT: M 57 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: N 21 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8017 (tttt) REVERT: N 57 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: O 43 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7389 (mptp) REVERT: O 45 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8269 (tppt) REVERT: O 57 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8018 (tm-30) outliers start: 62 outliers final: 29 residues processed: 224 average time/residue: 0.5720 time to fit residues: 135.2287 Evaluate side-chains 234 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 56 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 0.0670 chunk 73 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 overall best weight: 2.6324 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.111794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095156 restraints weight = 8947.166| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.11 r_work: 0.3260 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7575 Z= 0.157 Angle : 0.477 5.365 10215 Z= 0.280 Chirality : 0.051 0.127 1365 Planarity : 0.002 0.010 1245 Dihedral : 4.884 20.502 1080 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 6.41 % Allowed : 26.67 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR H 39 PHE 0.019 0.004 PHE I 94 HIS 0.003 0.001 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7575) covalent geometry : angle 0.47672 (10215) hydrogen bonds : bond 0.03254 ( 276) hydrogen bonds : angle 5.40969 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: B 23 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7545 (tttm) REVERT: B 57 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: B 64 THR cc_start: 0.9100 (m) cc_final: 0.8875 (m) REVERT: C 34 LYS cc_start: 0.8445 (mttt) cc_final: 0.8072 (mttt) REVERT: C 57 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: D 45 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8774 (ttpp) REVERT: D 57 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: E 57 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: F 20 GLU cc_start: 0.8315 (mp0) cc_final: 0.8042 (mt-10) REVERT: F 57 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: G 57 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: H 20 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8184 (mt-10) REVERT: H 45 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8645 (mtpt) REVERT: H 57 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: H 58 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8394 (mttp) REVERT: I 57 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: K 20 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8203 (mt-10) REVERT: K 34 LYS cc_start: 0.8601 (mttt) cc_final: 0.8274 (mttt) REVERT: K 57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: L 21 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.7900 (tmtt) REVERT: L 57 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: M 20 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: M 57 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: N 43 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7126 (mmtt) REVERT: N 57 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: O 45 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8220 (tppt) REVERT: O 57 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7982 (tm-30) outliers start: 49 outliers final: 19 residues processed: 215 average time/residue: 0.5717 time to fit residues: 129.4057 Evaluate side-chains 216 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.111272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094010 restraints weight = 8815.839| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.07 r_work: 0.3164 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 7575 Z= 0.384 Angle : 0.598 6.838 10215 Z= 0.353 Chirality : 0.057 0.143 1365 Planarity : 0.003 0.009 1245 Dihedral : 5.397 21.951 1080 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 8.10 % Allowed : 26.14 % Favored : 65.75 % 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: -2.19 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR M 39 PHE 0.018 0.004 PHE I 94 HIS 0.007 0.003 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00815 ( 7575) covalent geometry : angle 0.59804 (10215) hydrogen bonds : bond 0.03906 ( 276) hydrogen bonds : angle 5.48444 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7784 (tttm) REVERT: B 57 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: B 64 THR cc_start: 0.9173 (m) cc_final: 0.8965 (m) REVERT: C 57 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: D 57 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: E 57 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: G 57 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: H 20 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8168 (mt-10) REVERT: H 45 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8703 (mtpm) REVERT: H 57 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: H 58 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8306 (mttp) REVERT: I 57 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: J 57 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: K 20 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8160 (mt-10) REVERT: K 34 LYS cc_start: 0.8606 (mttt) cc_final: 0.8349 (mttt) REVERT: L 20 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8275 (mt-10) REVERT: L 21 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.7966 (tttt) REVERT: L 57 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: M 20 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: M 45 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8773 (mtpm) REVERT: M 57 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: N 57 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: O 45 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8288 (tppt) REVERT: O 57 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8012 (tm-30) outliers start: 62 outliers final: 29 residues processed: 217 average time/residue: 0.4862 time to fit residues: 111.2574 Evaluate side-chains 231 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097385 restraints weight = 8620.389| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.05 r_work: 0.3220 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 0.030 7575 Z= 0.237 Angle : 0.520 5.823 10215 Z= 0.305 Chirality : 0.053 0.130 1365 Planarity : 0.002 0.009 1245 Dihedral : 5.073 21.576 1080 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 6.54 % Allowed : 27.45 % Favored : 66.01 % 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: -2.26 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR H 39 PHE 0.018 0.004 PHE I 94 HIS 0.005 0.002 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7575) covalent geometry : angle 0.52016 (10215) hydrogen bonds : bond 0.03453 ( 276) hydrogen bonds : angle 5.40124 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7546 (tttm) REVERT: B 57 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: B 64 THR cc_start: 0.9139 (m) cc_final: 0.8923 (m) REVERT: C 57 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: D 45 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8767 (ttpp) REVERT: D 57 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: E 57 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: F 57 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: G 57 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: H 20 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8148 (mt-10) REVERT: H 45 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (mtpm) REVERT: H 57 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: H 58 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: I 57 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: J 57 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: K 20 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8183 (mt-10) REVERT: K 34 LYS cc_start: 0.8625 (mttt) cc_final: 0.8393 (mttt) REVERT: K 57 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: L 20 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8285 (mt-10) REVERT: L 21 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.7944 (tttt) REVERT: L 57 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: M 45 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8716 (mtpm) REVERT: M 57 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: N 57 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: O 45 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8260 (tppt) REVERT: O 57 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8016 (tm-30) outliers start: 50 outliers final: 25 residues processed: 211 average time/residue: 0.5184 time to fit residues: 115.4897 Evaluate side-chains 230 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 0.0010 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 overall best weight: 5.7994 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.112455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.095296 restraints weight = 8736.712| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7575 Z= 0.298 Angle : 0.554 6.242 10215 Z= 0.326 Chirality : 0.054 0.131 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.200 22.150 1080 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 6.93 % Allowed : 27.84 % Favored : 65.23 % 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: -2.33 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR H 39 PHE 0.018 0.004 PHE I 94 HIS 0.006 0.003 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 7575) covalent geometry : angle 0.55386 (10215) hydrogen bonds : bond 0.03676 ( 276) hydrogen bonds : angle 5.42698 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: B 23 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7584 (tttm) REVERT: B 57 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: C 57 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: D 57 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: E 57 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: F 57 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: G 57 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: H 20 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 57 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: H 58 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8366 (mttp) REVERT: I 57 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: J 57 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: K 20 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8179 (mt-10) REVERT: K 34 LYS cc_start: 0.8602 (mttt) cc_final: 0.8371 (mttt) REVERT: L 20 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8308 (mt-10) REVERT: L 21 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.7958 (tttt) REVERT: L 57 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: M 20 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8225 (mt-10) REVERT: M 45 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8760 (mtpm) REVERT: M 57 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: N 57 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: O 45 LYS cc_start: 0.9018 (ttpp) cc_final: 0.8260 (tppt) REVERT: O 57 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8020 (tm-30) outliers start: 53 outliers final: 30 residues processed: 214 average time/residue: 0.5082 time to fit residues: 114.4312 Evaluate side-chains 237 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096333 restraints weight = 8680.243| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7575 Z= 0.263 Angle : 0.533 5.900 10215 Z= 0.313 Chirality : 0.053 0.130 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.085 21.990 1080 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 6.54 % Allowed : 27.97 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR H 39 PHE 0.018 0.004 PHE N 94 HIS 0.005 0.002 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 7575) covalent geometry : angle 0.53280 (10215) hydrogen bonds : bond 0.03496 ( 276) hydrogen bonds : angle 5.40328 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: B 23 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7600 (tttm) REVERT: B 57 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: C 57 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: D 57 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: E 57 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: G 57 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: H 20 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8174 (mt-10) REVERT: H 45 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8749 (mtpt) REVERT: H 57 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: H 58 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8362 (mttp) REVERT: I 57 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: J 57 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: K 20 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8193 (mt-10) REVERT: K 34 LYS cc_start: 0.8612 (mttt) cc_final: 0.8377 (mttt) REVERT: L 20 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8309 (mt-10) REVERT: L 21 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.7955 (tttt) REVERT: L 57 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: M 20 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8305 (mt-10) REVERT: M 45 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (mtpm) REVERT: M 57 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: N 57 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: O 45 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8286 (tppt) REVERT: O 57 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7995 (tm-30) outliers start: 50 outliers final: 30 residues processed: 213 average time/residue: 0.4565 time to fit residues: 102.4534 Evaluate side-chains 235 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.115727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098547 restraints weight = 8429.926| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.04 r_work: 0.3239 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7575 Z= 0.199 Angle : 0.498 5.414 10215 Z= 0.292 Chirality : 0.052 0.129 1365 Planarity : 0.002 0.009 1245 Dihedral : 4.890 21.462 1080 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.75 % Allowed : 28.76 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR H 39 PHE 0.018 0.004 PHE N 94 HIS 0.004 0.002 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7575) covalent geometry : angle 0.49844 (10215) hydrogen bonds : bond 0.03281 ( 276) hydrogen bonds : angle 5.36813 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: B 23 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7618 (tttm) REVERT: B 57 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: B 64 THR cc_start: 0.9127 (m) cc_final: 0.8910 (m) REVERT: C 57 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: D 57 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: E 57 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: F 39 TYR cc_start: 0.9185 (m-80) cc_final: 0.8937 (m-80) REVERT: F 43 LYS cc_start: 0.7701 (mptp) cc_final: 0.7406 (mptp) REVERT: F 57 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: G 57 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: H 20 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8156 (mt-10) REVERT: H 45 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8736 (mtpt) REVERT: H 57 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: H 58 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8371 (mttp) REVERT: I 57 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: K 20 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8197 (mt-10) REVERT: K 34 LYS cc_start: 0.8614 (mttt) cc_final: 0.8364 (mttt) REVERT: K 57 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: L 20 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8306 (mt-10) REVERT: L 21 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: L 57 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: M 20 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8273 (mt-10) REVERT: M 45 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (mtpm) REVERT: M 57 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: N 57 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: O 45 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8283 (tppt) REVERT: O 57 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7957 (tm-30) outliers start: 44 outliers final: 25 residues processed: 212 average time/residue: 0.4925 time to fit residues: 110.1403 Evaluate side-chains 231 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 0.4980 chunk 72 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.119292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102172 restraints weight = 8362.476| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.04 r_work: 0.3309 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7575 Z= 0.128 Angle : 0.460 4.945 10215 Z= 0.270 Chirality : 0.051 0.127 1365 Planarity : 0.002 0.009 1245 Dihedral : 4.572 20.476 1080 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.97 % Allowed : 29.41 % Favored : 65.62 % 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: -2.23 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR H 39 PHE 0.018 0.004 PHE N 94 HIS 0.003 0.001 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7575) covalent geometry : angle 0.45990 (10215) hydrogen bonds : bond 0.02948 ( 276) hydrogen bonds : angle 5.29449 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: B 20 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 23 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7602 (tttm) REVERT: B 57 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: C 57 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7700 (mm-30) REVERT: D 57 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: E 57 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: F 20 GLU cc_start: 0.8400 (mp0) cc_final: 0.8151 (mt-10) REVERT: F 39 TYR cc_start: 0.9167 (m-80) cc_final: 0.8921 (m-80) REVERT: F 57 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: G 57 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: H 20 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8142 (mt-10) REVERT: H 45 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8726 (mtpt) REVERT: H 57 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: I 42 SER cc_start: 0.8990 (t) cc_final: 0.8593 (p) REVERT: I 57 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: J 45 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8062 (tppt) REVERT: K 20 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8250 (mt-10) REVERT: K 34 LYS cc_start: 0.8645 (mttt) cc_final: 0.8383 (mttt) REVERT: K 57 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: L 20 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8265 (mt-10) REVERT: L 21 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.7935 (tttt) REVERT: L 57 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: M 20 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8243 (mt-10) REVERT: M 45 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8732 (mtpm) REVERT: M 57 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: N 57 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: O 45 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8208 (tppt) REVERT: O 57 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7913 (tm-30) outliers start: 38 outliers final: 19 residues processed: 204 average time/residue: 0.5797 time to fit residues: 124.5002 Evaluate side-chains 213 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.110409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093358 restraints weight = 8753.604| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.06 r_work: 0.3159 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.046 7575 Z= 0.429 Angle : 0.623 6.840 10215 Z= 0.368 Chirality : 0.058 0.180 1365 Planarity : 0.003 0.009 1245 Dihedral : 5.289 22.085 1080 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.75 % Allowed : 29.41 % Favored : 64.84 % 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: -2.39 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR M 39 PHE 0.017 0.004 PHE I 94 HIS 0.009 0.004 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00909 ( 7575) covalent geometry : angle 0.62289 (10215) hydrogen bonds : bond 0.03901 ( 276) hydrogen bonds : angle 5.40612 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.81 seconds wall clock time: 52 minutes 36.21 seconds (3156.21 seconds total)