Starting phenix.real_space_refine on Tue Feb 3 22:39:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hc9_52041/02_2026/9hc9_52041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hc9_52041/02_2026/9hc9_52041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hc9_52041/02_2026/9hc9_52041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hc9_52041/02_2026/9hc9_52041.map" model { file = "/net/cci-nas-00/data/ceres_data/9hc9_52041/02_2026/9hc9_52041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hc9_52041/02_2026/9hc9_52041.cif" } resolution = 2.76 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= 0.002 sd= 0.015 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 30 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: 0.76, per 1000 atoms: 0.10 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: 0.61 Conformation dependent library (CDL) restraints added in 361.1 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: 0.35 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: 8.050A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.533A 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: 6.539A 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: 6.524A 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: 8.031A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.390A 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: 5.977A 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: 5.992A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 5.977A 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: 6.796A 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: 6.799A 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: 6.797A 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: 9.951A 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: 6.418A pdb=" N VAL A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.991A 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: 8.809A 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: 9.016A 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: 6.426A 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: 6.536A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.492A 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: 9.949A 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: 9.365A pdb=" N THR D 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.408A 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: 6.527A 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: 6.484A 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: 9.951A 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: 9.372A pdb=" N THR E 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL D 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.992A 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: 6.615A 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: 6.616A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 8.050A 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: 6.390A 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: 8.031A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU H 20 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 6.615A 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: 5.977A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 5.978A 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: 6.796A pdb=" N TYR G 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY G 41 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.797A 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: 6.714A pdb=" N THR F 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.651A 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: 6.757A 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: 6.714A 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: 6.757A 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: 6.796A pdb=" N TYR J 39 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL I 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.757A 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: 6.798A pdb=" N LYS J 43 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.713A 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: 9.011A pdb=" N THR F 72 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR G 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL F 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL G 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.910A 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: 8.805A 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: 9.011A 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: 7.990A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.533A 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: 6.533A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN I 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.491A 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: 7.991A 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: 7.909A pdb=" N GLN J 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.491A 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: 6.532A 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: 6.533A pdb=" N ALA L 18 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 8.031A 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: 6.534A pdb=" N ALA M 18 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 8.033A 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: 6.387A 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: 5.977A 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: 5.973A pdb=" N LYS M 34 " --> pdb=" O GLU N 35 " (cutoff:3.500A) removed outlier: 5.980A 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: 6.796A 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: 6.798A 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: 6.796A 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: 6.798A 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: 6.795A 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: 9.371A pdb=" N THR L 75 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL K 74 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 7.991A 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: 6.491A 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: 6.418A pdb=" N VAL L 74 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 7.991A 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: 7.910A pdb=" N GLN M 79 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.490A 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: 9.011A pdb=" N THR M 72 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR N 75 " --> pdb=" O THR M 72 " (cutoff:3.500A) removed outlier: 6.419A 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: 6.534A pdb=" N ALA M 76 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN N 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA M 78 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 8.807A 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: 9.013A pdb=" N THR N 72 " --> pdb=" O GLY O 73 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N THR O 75 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL N 74 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 7.990A 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: 7.909A 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: 1.35 Time building geometry restraints manager: 0.87 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: 1119 1.33 - 1.41: 261 1.41 - 1.48: 1305 1.48 - 1.55: 3570 Bond restraints: 7575 Sorted by residual: bond pdb=" C GLY J 73 " pdb=" O GLY J 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 I 73 " pdb=" O GLY I 73 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.12e-02 7.97e+03 1.72e+01 bond pdb=" C GLY G 73 " pdb=" O GLY G 73 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.12e-02 7.97e+03 1.71e+01 bond pdb=" C GLY E 73 " pdb=" O GLY E 73 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.12e-02 7.97e+03 1.71e+01 bond pdb=" C GLY O 73 " pdb=" O GLY O 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: 7755 1.96 - 3.93: 1910 3.93 - 5.89: 370 5.89 - 7.85: 120 7.85 - 9.82: 60 Bond angle restraints: 10215 Sorted by residual: angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 110.62 100.80 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 M 74 " pdb=" CA VAL M 74 " pdb=" C VAL M 74 " ideal model delta sigma weight residual 110.62 100.83 9.79 1.02e+00 9.61e-01 9.22e+01 angle pdb=" N VAL N 74 " pdb=" CA VAL N 74 " pdb=" C VAL N 74 " ideal model delta sigma weight residual 110.62 100.84 9.78 1.02e+00 9.61e-01 9.19e+01 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 110.62 100.84 9.78 1.02e+00 9.61e-01 9.19e+01 ... (remaining 10210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 3825 17.10 - 34.20: 390 34.20 - 51.30: 150 51.30 - 68.40: 75 68.40 - 85.50: 30 Dihedral angle restraints: 4470 sinusoidal: 1500 harmonic: 2970 Sorted by residual: dihedral pdb=" C HIS K 50 " pdb=" N HIS K 50 " pdb=" CA HIS K 50 " pdb=" CB HIS K 50 " ideal model delta harmonic sigma weight residual -122.60 -132.30 9.70 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS N 50 " pdb=" N HIS N 50 " pdb=" CA HIS N 50 " pdb=" CB HIS N 50 " ideal model delta harmonic sigma weight residual -122.60 -132.29 9.69 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS B 50 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " pdb=" CB HIS B 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: 1035 0.098 - 0.196: 285 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 E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA HIS K 50 " pdb=" N HIS K 50 " pdb=" C HIS K 50 " pdb=" CB HIS K 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 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 ... (remaining 1362 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 72 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C THR D 72 " 0.039 2.00e-02 2.50e+03 pdb=" O THR D 72 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 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 2.21e-02 4.90e+00 pdb=" C THR K 72 " -0.038 2.00e-02 2.50e+03 pdb=" O THR K 72 " 0.014 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 E 72 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C THR E 72 " 0.038 2.00e-02 2.50e+03 pdb=" O THR E 72 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY E 73 " -0.013 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 60 1.91 - 2.65: 239 2.65 - 3.40: 9187 3.40 - 4.15: 19629 4.15 - 4.90: 35927 Nonbonded interactions: 65042 Sorted by model distance: nonbonded pdb=" CE1 PHE B 94 " pdb=" OE2 GLU C 61 " model vdw 1.158 3.340 nonbonded pdb=" CE1 PHE M 94 " pdb=" OE2 GLU N 61 " model vdw 1.169 3.340 nonbonded pdb=" CE1 PHE A 94 " pdb=" OE2 GLU B 61 " model vdw 1.169 3.340 nonbonded pdb=" CE1 PHE H 94 " pdb=" OE2 GLU I 61 " model vdw 1.169 3.340 nonbonded pdb=" CE1 PHE I 94 " pdb=" OE2 GLU J 61 " model vdw 1.169 3.340 ... (remaining 65037 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 2.026 9.818 10215 Z= 1.402 Chirality : 0.094 0.489 1365 Planarity : 0.005 0.022 1245 Dihedral : 19.887 85.501 2580 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.39 % Allowed : 29.02 % Favored : 70.59 % 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 : 0.09 (0.22), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR K 39 PHE 0.025 0.007 PHE C 94 HIS 0.008 0.005 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.01443 ( 7575) covalent geometry : angle 2.02576 (10215) hydrogen bonds : bond 0.11897 ( 276) hydrogen bonds : angle 8.07121 ( 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 226 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.7499 (mp0) cc_final: 0.7298 (mp0) REVERT: G 20 GLU cc_start: 0.7442 (mp0) cc_final: 0.7217 (mp0) REVERT: I 20 GLU cc_start: 0.7619 (mp0) cc_final: 0.7347 (mp0) REVERT: L 20 GLU cc_start: 0.7476 (mp0) cc_final: 0.7235 (mp0) REVERT: L 57 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7641 (tt0) REVERT: N 57 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7749 (tt0) outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.5800 time to fit residues: 136.1485 Evaluate side-chains 193 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN H 79 GLN N 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.117663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098326 restraints weight = 8683.517| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.28 r_work: 0.3384 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7575 Z= 0.231 Angle : 0.573 7.960 10215 Z= 0.341 Chirality : 0.055 0.140 1365 Planarity : 0.003 0.013 1245 Dihedral : 5.629 21.961 1080 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.45 % Allowed : 22.75 % Favored : 69.80 % 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: -1.38 (0.24), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR O 39 PHE 0.023 0.006 PHE I 94 HIS 0.005 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 7575) covalent geometry : angle 0.57338 (10215) hydrogen bonds : bond 0.03756 ( 276) hydrogen bonds : angle 5.77256 ( 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 205 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 0.311 Fit side-chains REVERT: A 34 LYS cc_start: 0.8089 (mttt) cc_final: 0.7828 (mtmt) REVERT: A 43 LYS cc_start: 0.8753 (tttm) cc_final: 0.8538 (tttt) REVERT: C 45 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8316 (tttp) REVERT: E 45 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8399 (tttp) REVERT: H 45 LYS cc_start: 0.8762 (mtpm) cc_final: 0.8419 (tttp) REVERT: J 45 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8565 (tttp) REVERT: K 44 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (t) REVERT: L 44 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8744 (t) REVERT: M 45 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8277 (tttp) REVERT: N 45 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8268 (tttp) REVERT: O 45 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8469 (tttp) outliers start: 57 outliers final: 28 residues processed: 182 average time/residue: 0.6076 time to fit residues: 115.5554 Evaluate side-chains 162 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS 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: 10.0000 chunk 53 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 39 optimal weight: 0.0070 chunk 83 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 7.2006 ------------------------------------------------------------------------------- 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 = 0.106250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.087297 restraints weight = 9293.984| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.31 r_work: 0.3208 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 7575 Z= 0.378 Angle : 0.637 7.462 10215 Z= 0.369 Chirality : 0.057 0.147 1365 Planarity : 0.003 0.010 1245 Dihedral : 5.804 23.373 1080 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 7.45 % Allowed : 18.04 % Favored : 74.51 % 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 (0.24), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.018 0.004 PHE J 94 HIS 0.007 0.003 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 7575) covalent geometry : angle 0.63669 (10215) hydrogen bonds : bond 0.04095 ( 276) hydrogen bonds : angle 5.38238 ( 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 210 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.187 Fit side-chains REVERT: A 34 LYS cc_start: 0.8155 (mttt) cc_final: 0.7889 (mttt) REVERT: A 43 LYS cc_start: 0.8844 (tttm) cc_final: 0.8571 (tmtt) REVERT: A 80 LYS cc_start: 0.9389 (mttp) cc_final: 0.9096 (mttm) REVERT: A 83 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8070 (mt-10) REVERT: C 45 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8233 (ttmt) REVERT: D 20 GLU cc_start: 0.7946 (mp0) cc_final: 0.7510 (mp0) REVERT: E 45 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8346 (ttmp) REVERT: H 45 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8352 (tttp) REVERT: J 45 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8524 (ttmp) REVERT: M 45 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.7986 (mptt) REVERT: N 83 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8023 (mt-10) REVERT: O 45 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8499 (tttp) outliers start: 57 outliers final: 45 residues processed: 182 average time/residue: 0.5556 time to fit residues: 105.9255 Evaluate side-chains 198 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 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: 0.9980 chunk 101 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.108462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.089758 restraints weight = 9320.440| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.33 r_work: 0.3255 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7575 Z= 0.254 Angle : 0.544 5.967 10215 Z= 0.316 Chirality : 0.053 0.137 1365 Planarity : 0.002 0.008 1245 Dihedral : 5.280 22.724 1080 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 6.93 % Allowed : 18.95 % Favored : 74.12 % 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: -1.95 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR J 39 PHE 0.013 0.003 PHE N 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 7575) covalent geometry : angle 0.54367 (10215) hydrogen bonds : bond 0.03551 ( 276) hydrogen bonds : angle 5.28152 ( 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 190 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.267 Fit side-chains REVERT: A 34 LYS cc_start: 0.8167 (mttt) cc_final: 0.7941 (mttt) REVERT: A 43 LYS cc_start: 0.8865 (tttm) cc_final: 0.8593 (tmtt) REVERT: B 45 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8459 (ttmp) REVERT: C 45 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8327 (ttmt) REVERT: D 20 GLU cc_start: 0.8019 (mp0) cc_final: 0.7601 (mp0) REVERT: D 45 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8321 (tmmt) REVERT: E 45 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8377 (ttmp) REVERT: F 57 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: H 45 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8386 (tttp) REVERT: J 45 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8587 (ttmp) REVERT: M 45 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8049 (mptt) REVERT: N 45 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8326 (tttp) REVERT: O 45 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8575 (tttp) outliers start: 53 outliers final: 41 residues processed: 171 average time/residue: 0.6008 time to fit residues: 107.5283 Evaluate side-chains 184 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 THR 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: 9.9990 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.086397 restraints weight = 9515.170| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.32 r_work: 0.3194 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 7575 Z= 0.370 Angle : 0.614 7.527 10215 Z= 0.357 Chirality : 0.056 0.141 1365 Planarity : 0.003 0.010 1245 Dihedral : 5.640 23.787 1080 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 7.32 % Allowed : 18.56 % Favored : 74.12 % 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: -2.22 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 39 PHE 0.013 0.003 PHE J 94 HIS 0.005 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00765 ( 7575) covalent geometry : angle 0.61362 (10215) hydrogen bonds : bond 0.03800 ( 276) hydrogen bonds : angle 5.21225 ( 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 202 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.191 Fit side-chains REVERT: A 43 LYS cc_start: 0.8787 (tttm) cc_final: 0.8492 (tmtt) REVERT: A 80 LYS cc_start: 0.9394 (mtpp) cc_final: 0.9050 (mttm) REVERT: A 83 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 45 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8452 (ttmp) REVERT: C 45 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8199 (ttmt) REVERT: D 20 GLU cc_start: 0.8017 (mp0) cc_final: 0.7554 (mp0) REVERT: E 45 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8388 (ttmp) REVERT: H 45 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8315 (tttp) REVERT: J 45 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8508 (tttp) REVERT: M 45 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7941 (mptt) REVERT: N 45 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8376 (mtpm) REVERT: N 83 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7913 (mt-10) REVERT: O 45 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8502 (tttp) outliers start: 56 outliers final: 45 residues processed: 180 average time/residue: 0.5372 time to fit residues: 101.3384 Evaluate side-chains 197 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090121 restraints weight = 9242.976| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.29 r_work: 0.3256 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7575 Z= 0.235 Angle : 0.533 6.971 10215 Z= 0.309 Chirality : 0.053 0.133 1365 Planarity : 0.002 0.008 1245 Dihedral : 5.176 22.686 1080 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 6.93 % Allowed : 19.35 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 39 PHE 0.013 0.003 PHE D 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 7575) covalent geometry : angle 0.53280 (10215) hydrogen bonds : bond 0.03399 ( 276) hydrogen bonds : angle 5.22013 ( 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 188 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.261 Fit side-chains REVERT: A 43 LYS cc_start: 0.8867 (tttm) cc_final: 0.8587 (tmtt) REVERT: B 45 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8447 (ttmp) REVERT: C 45 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8314 (ttmt) REVERT: D 20 GLU cc_start: 0.8019 (mp0) cc_final: 0.7580 (mp0) REVERT: D 45 LYS cc_start: 0.8942 (tttp) cc_final: 0.8429 (tmmt) REVERT: E 45 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8358 (ttmp) REVERT: H 45 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8337 (tttp) REVERT: J 45 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8554 (tttp) REVERT: L 83 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8120 (mt-10) REVERT: N 45 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8306 (tttp) REVERT: O 45 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8575 (tttp) outliers start: 53 outliers final: 43 residues processed: 169 average time/residue: 0.5589 time to fit residues: 98.9414 Evaluate side-chains 183 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086188 restraints weight = 9503.747| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.30 r_work: 0.3196 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 7575 Z= 0.369 Angle : 0.611 7.671 10215 Z= 0.356 Chirality : 0.056 0.141 1365 Planarity : 0.003 0.010 1245 Dihedral : 5.569 23.661 1080 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.32 % Allowed : 18.30 % Favored : 74.38 % 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: -2.38 (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 0.012 0.002 TYR G 39 PHE 0.013 0.003 PHE J 94 HIS 0.005 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00764 ( 7575) covalent geometry : angle 0.61083 (10215) hydrogen bonds : bond 0.03734 ( 276) hydrogen bonds : angle 5.21866 ( 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 203 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 0.203 Fit side-chains REVERT: A 43 LYS cc_start: 0.8810 (tttm) cc_final: 0.8544 (tmtt) REVERT: A 80 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9071 (mttm) REVERT: A 83 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8054 (mt-10) REVERT: B 45 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8461 (ttmp) REVERT: C 45 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8267 (ttmt) REVERT: D 20 GLU cc_start: 0.8075 (mp0) cc_final: 0.7642 (mp0) REVERT: E 45 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8385 (ttmp) REVERT: H 45 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8360 (tttp) REVERT: J 45 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8525 (tttp) REVERT: M 45 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7950 (mptt) REVERT: N 45 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8417 (mtpm) REVERT: N 83 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7883 (mt-10) REVERT: O 45 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8529 (tttp) outliers start: 56 outliers final: 44 residues processed: 181 average time/residue: 0.5163 time to fit residues: 97.7812 Evaluate side-chains 198 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 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: 5.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 103 optimal weight: 5.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.107142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088619 restraints weight = 9317.109| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.30 r_work: 0.3237 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7575 Z= 0.262 Angle : 0.549 7.303 10215 Z= 0.318 Chirality : 0.053 0.135 1365 Planarity : 0.002 0.008 1245 Dihedral : 5.245 22.802 1080 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.80 % Allowed : 19.48 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 39 PHE 0.013 0.003 PHE D 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 7575) covalent geometry : angle 0.54900 (10215) hydrogen bonds : bond 0.03441 ( 276) hydrogen bonds : angle 5.22683 ( 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 195 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.281 Fit side-chains REVERT: A 43 LYS cc_start: 0.8860 (tttm) cc_final: 0.8569 (tmtt) REVERT: B 45 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8446 (ttmp) REVERT: C 45 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8337 (ttmt) REVERT: D 20 GLU cc_start: 0.8043 (mp0) cc_final: 0.7575 (mp0) REVERT: E 45 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8373 (ttmp) REVERT: H 43 LYS cc_start: 0.8578 (tttm) cc_final: 0.8341 (tttp) REVERT: H 45 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8379 (tttp) REVERT: I 83 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7997 (mt-10) REVERT: J 45 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8558 (tttp) REVERT: N 45 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8275 (tttp) REVERT: N 83 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7872 (mt-10) REVERT: O 45 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8543 (tttp) outliers start: 52 outliers final: 44 residues processed: 175 average time/residue: 0.5687 time to fit residues: 104.3800 Evaluate side-chains 194 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087192 restraints weight = 9368.591| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.29 r_work: 0.3223 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 7575 Z= 0.314 Angle : 0.581 7.539 10215 Z= 0.337 Chirality : 0.055 0.134 1365 Planarity : 0.002 0.009 1245 Dihedral : 5.376 23.334 1080 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 6.80 % Allowed : 19.74 % Favored : 73.46 % 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: -2.46 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 39 PHE 0.013 0.003 PHE D 94 HIS 0.005 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 7575) covalent geometry : angle 0.58121 (10215) hydrogen bonds : bond 0.03573 ( 276) hydrogen bonds : angle 5.22099 ( 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 198 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.219 Fit side-chains REVERT: A 43 LYS cc_start: 0.8840 (tttm) cc_final: 0.8571 (tmtt) REVERT: B 45 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (ttmp) REVERT: C 45 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8318 (ttmt) REVERT: D 20 GLU cc_start: 0.8080 (mp0) cc_final: 0.7609 (mp0) REVERT: E 45 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8421 (ttmp) REVERT: H 43 LYS cc_start: 0.8590 (tttm) cc_final: 0.8360 (tttp) REVERT: H 45 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8387 (tttp) REVERT: I 83 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8038 (mt-10) REVERT: J 45 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8555 (tttp) REVERT: N 45 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8292 (tttp) REVERT: N 83 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7873 (mt-10) REVERT: O 45 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8549 (tttp) outliers start: 52 outliers final: 44 residues processed: 179 average time/residue: 0.5443 time to fit residues: 102.0293 Evaluate side-chains 197 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.106044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087575 restraints weight = 9383.429| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.31 r_work: 0.3232 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 7575 Z= 0.296 Angle : 0.571 7.549 10215 Z= 0.331 Chirality : 0.054 0.135 1365 Planarity : 0.002 0.008 1245 Dihedral : 5.308 22.880 1080 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.80 % Allowed : 19.87 % Favored : 73.33 % 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: -2.46 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 39 PHE 0.013 0.003 PHE N 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 7575) covalent geometry : angle 0.57097 (10215) hydrogen bonds : bond 0.03505 ( 276) hydrogen bonds : angle 5.21169 ( 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 199 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.330 Fit side-chains REVERT: A 43 LYS cc_start: 0.8850 (tttm) cc_final: 0.8565 (tmtt) REVERT: B 45 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8457 (ttmp) REVERT: C 45 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8319 (ttmt) REVERT: D 20 GLU cc_start: 0.8087 (mp0) cc_final: 0.7612 (mp0) REVERT: E 45 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8375 (ttmp) REVERT: H 43 LYS cc_start: 0.8574 (tttm) cc_final: 0.8340 (tttm) REVERT: H 45 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8413 (tttp) REVERT: I 83 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8103 (mt-10) REVERT: J 45 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8561 (tttp) REVERT: M 61 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7014 (mt-10) REVERT: N 45 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8296 (tttp) REVERT: N 83 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7885 (mt-10) REVERT: O 45 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8549 (tttp) outliers start: 52 outliers final: 44 residues processed: 180 average time/residue: 0.6346 time to fit residues: 119.7276 Evaluate side-chains 197 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 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 = 0.3583 r_free = 0.3583 target = 0.103732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085355 restraints weight = 9454.346| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.28 r_work: 0.3199 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 7575 Z= 0.393 Angle : 0.636 8.216 10215 Z= 0.367 Chirality : 0.057 0.142 1365 Planarity : 0.003 0.011 1245 Dihedral : 5.588 23.968 1080 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 6.80 % Allowed : 19.87 % Favored : 73.33 % 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: -2.51 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 39 PHE 0.013 0.002 PHE J 94 HIS 0.006 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00812 ( 7575) covalent geometry : angle 0.63629 (10215) hydrogen bonds : bond 0.03777 ( 276) hydrogen bonds : angle 5.26435 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2732.09 seconds wall clock time: 47 minutes 23.76 seconds (2843.76 seconds total)