Starting phenix.real_space_refine on Tue Feb 3 16:34:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hc8_52040/02_2026/9hc8_52040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hc8_52040/02_2026/9hc8_52040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hc8_52040/02_2026/9hc8_52040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hc8_52040/02_2026/9hc8_52040.map" model { file = "/net/cci-nas-00/data/ceres_data/9hc8_52040/02_2026/9hc8_52040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hc8_52040/02_2026/9hc8_52040.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 3160 2.51 5 N 870 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 5040 Number of models: 1 Model: "" Number of chains: 10 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "G" 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 Chain: "H" 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 Chain: "I" 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 Chain: "J" 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 Time building chain proxies: 1.13, per 1000 atoms: 0.22 Number of scatterers: 5040 At special positions: 0 Unit cell: (147, 90.3, 47.25, 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 1010 8.00 N 870 7.00 C 3160 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: 0.37 Conformation dependent library (CDL) restraints added in 232.8 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.607A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA C 19 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS C 21 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU B 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA D 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LYS D 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C 20 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.400A 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 49 removed outlier: 5.933A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL B 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLY A 36 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N TYR B 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N GLY B 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL A 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N LYS B 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N SER A 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N LYS B 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR A 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY B 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL C 37 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLY B 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR C 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N GLY C 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL B 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N LYS C 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N SER B 42 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N LYS C 45 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR B 44 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY C 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU B 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL C 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL D 37 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLY C 36 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N TYR D 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N GLY D 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N LYS D 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N SER C 42 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N LYS D 45 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR C 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY D 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU C 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL D 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL E 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY D 36 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR E 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N LYS E 45 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR D 44 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY E 47 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU D 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL E 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 79 removed outlier: 6.828A pdb=" N VAL B 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA C 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA C 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN B 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL D 71 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY D 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL E 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR D 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY E 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 92 Processing sheet with id=AA7, 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: 8.048A pdb=" N ALA G 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.529A 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: 6.622A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA H 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL H 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA I 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA H 18 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU H 20 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL I 16 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA J 19 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA I 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS J 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU I 20 " --> pdb=" O LYS J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 34 through 49 removed outlier: 5.933A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL G 37 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLY F 36 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 10.001A pdb=" N TYR G 39 " --> pdb=" O GLY F 36 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 10.046A pdb=" N LYS G 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N SER F 42 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LYS G 45 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR F 44 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLY G 47 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU F 46 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL G 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL F 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL H 37 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY G 36 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 10.001A pdb=" N TYR H 39 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N GLY H 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL G 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N LYS H 43 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N SER G 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N LYS H 45 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR G 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLY H 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU G 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL H 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL G 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL I 37 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY H 36 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N TYR I 39 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LEU H 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N GLY I 41 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL H 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 10.046A pdb=" N LYS I 43 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N SER H 42 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LYS I 45 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR H 44 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLY I 47 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU H 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL I 49 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL H 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL J 37 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY I 36 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR J 39 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N LYS J 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N SER I 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N LYS J 45 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR I 44 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY J 47 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU I 46 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL J 49 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL I 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 52 through 57 Processing sheet with id=AB1, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB2, first strand: chain 'F' and resid 70 through 79 removed outlier: 6.822A pdb=" N VAL G 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR F 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY G 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL F 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL H 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR G 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY H 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL I 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR H 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY I 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL H 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR I 75 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA J 76 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL I 77 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA J 78 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN I 79 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 92 166 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.27: 880 1.27 - 1.34: 760 1.34 - 1.41: 170 1.41 - 1.49: 982 1.49 - 1.56: 2258 Bond restraints: 5050 Sorted by residual: bond pdb=" CA GLY G 73 " pdb=" C GLY G 73 " ideal model delta sigma weight residual 1.515 1.466 0.050 9.30e-03 1.16e+04 2.85e+01 bond pdb=" CA GLY D 73 " pdb=" C GLY D 73 " ideal model delta sigma weight residual 1.515 1.466 0.050 9.30e-03 1.16e+04 2.84e+01 bond pdb=" CA GLY H 73 " pdb=" C GLY H 73 " ideal model delta sigma weight residual 1.515 1.466 0.050 9.30e-03 1.16e+04 2.83e+01 bond pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 1.515 1.466 0.049 9.30e-03 1.16e+04 2.82e+01 bond pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 1.515 1.466 0.049 9.30e-03 1.16e+04 2.81e+01 ... (remaining 5045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 5612 2.46 - 4.91: 1067 4.91 - 7.37: 61 7.37 - 9.83: 55 9.83 - 12.28: 15 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL G 74 " pdb=" CA VAL G 74 " pdb=" C VAL G 74 " ideal model delta sigma weight residual 110.72 98.44 12.28 1.01e+00 9.80e-01 1.48e+02 angle pdb=" N VAL I 74 " pdb=" CA VAL I 74 " pdb=" C VAL I 74 " ideal model delta sigma weight residual 110.72 98.46 12.26 1.01e+00 9.80e-01 1.47e+02 angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 110.72 98.46 12.26 1.01e+00 9.80e-01 1.47e+02 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 110.72 98.46 12.26 1.01e+00 9.80e-01 1.47e+02 angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 110.72 98.48 12.24 1.01e+00 9.80e-01 1.47e+02 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 2550 16.82 - 33.63: 240 33.63 - 50.45: 144 50.45 - 67.27: 26 67.27 - 84.08: 20 Dihedral angle restraints: 2980 sinusoidal: 1000 harmonic: 1980 Sorted by residual: dihedral pdb=" C HIS I 50 " pdb=" N HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C HIS G 50 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " pdb=" CB HIS G 50 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C HIS D 50 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " pdb=" CB HIS D 50 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 697 0.098 - 0.197: 193 0.197 - 0.295: 10 0.295 - 0.394: 0 0.394 - 0.492: 10 Chirality restraints: 910 Sorted by residual: chirality pdb=" CA HIS D 50 " pdb=" N HIS D 50 " pdb=" C HIS D 50 " pdb=" CB HIS D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA HIS I 50 " pdb=" N HIS I 50 " pdb=" C HIS I 50 " pdb=" CB HIS I 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.04e+00 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 6.03e+00 ... (remaining 907 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 71 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C VAL B 71 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL B 71 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 72 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 71 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C VAL F 71 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL F 71 " 0.012 2.00e-02 2.50e+03 pdb=" N THR F 72 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 71 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C VAL H 71 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL H 71 " 0.012 2.00e-02 2.50e+03 pdb=" N THR H 72 " 0.011 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1871 2.87 - 3.37: 3973 3.37 - 3.88: 9270 3.88 - 4.39: 10212 4.39 - 4.90: 18640 Nonbonded interactions: 43966 Sorted by model distance: nonbonded pdb=" NZ LYS E 80 " pdb=" OE2 GLU E 83 " model vdw 2.357 3.120 nonbonded pdb=" NZ LYS G 80 " pdb=" OE2 GLU G 83 " model vdw 2.357 3.120 nonbonded pdb=" NZ LYS A 80 " pdb=" OE2 GLU A 83 " model vdw 2.357 3.120 nonbonded pdb=" NZ LYS C 80 " pdb=" OE2 GLU C 83 " model vdw 2.357 3.120 nonbonded pdb=" NZ LYS J 80 " pdb=" OE2 GLU J 83 " model vdw 2.357 3.120 ... (remaining 43961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.061 5050 Z= 1.293 Angle : 2.009 12.285 6810 Z= 1.397 Chirality : 0.097 0.492 910 Planarity : 0.006 0.019 830 Dihedral : 19.574 84.082 1720 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 37.25 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.33), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.09 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.004 TYR B 39 PHE 0.029 0.008 PHE D 94 HIS 0.008 0.005 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.01678 ( 5050) covalent geometry : angle 2.00893 ( 6810) hydrogen bonds : bond 0.08824 ( 166) hydrogen bonds : angle 7.16164 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.227 Fit side-chains REVERT: C 33 THR cc_start: 0.7216 (t) cc_final: 0.6729 (m) REVERT: D 33 THR cc_start: 0.6979 (t) cc_final: 0.6749 (m) REVERT: E 33 THR cc_start: 0.7205 (t) cc_final: 0.6706 (m) REVERT: F 46 GLU cc_start: 0.7619 (tt0) cc_final: 0.7291 (tm-30) REVERT: H 43 LYS cc_start: 0.7786 (tttt) cc_final: 0.7475 (tttm) REVERT: H 46 GLU cc_start: 0.7591 (tt0) cc_final: 0.7305 (tm-30) REVERT: I 80 LYS cc_start: 0.9084 (mttm) cc_final: 0.8862 (mtpp) REVERT: J 43 LYS cc_start: 0.7945 (tttt) cc_final: 0.7734 (tttp) REVERT: J 96 LYS cc_start: 0.8013 (mttt) cc_final: 0.7809 (mttt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.5282 time to fit residues: 70.4347 Evaluate side-chains 105 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 65 ASN C 50 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 79 GLN J 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.111522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095902 restraints weight = 6496.435| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.18 r_work: 0.3391 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5050 Z= 0.235 Angle : 0.553 6.935 6810 Z= 0.313 Chirality : 0.054 0.131 910 Planarity : 0.002 0.011 830 Dihedral : 5.812 24.212 720 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.86 % Allowed : 28.24 % Favored : 64.90 % 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: -1.19 (0.30), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR B 39 PHE 0.013 0.003 PHE E 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5050) covalent geometry : angle 0.55272 ( 6810) hydrogen bonds : bond 0.03196 ( 166) hydrogen bonds : angle 5.22668 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.202 Fit side-chains REVERT: A 34 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7790 (mtpt) REVERT: B 44 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8534 (m) REVERT: C 60 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6824 (ttmm) REVERT: D 21 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7856 (tttt) REVERT: D 45 LYS cc_start: 0.8071 (mtpm) cc_final: 0.7553 (ttmm) REVERT: D 60 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7075 (tttt) REVERT: E 45 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7378 (tppt) REVERT: E 60 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7212 (ttmp) REVERT: F 43 LYS cc_start: 0.8456 (tttt) cc_final: 0.8103 (tttm) REVERT: F 46 GLU cc_start: 0.8176 (tt0) cc_final: 0.7565 (tm-30) REVERT: H 43 LYS cc_start: 0.8120 (tttt) cc_final: 0.7751 (tttm) REVERT: H 60 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.5964 (mptp) REVERT: J 45 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7603 (ttpt) outliers start: 35 outliers final: 19 residues processed: 107 average time/residue: 0.4226 time to fit residues: 47.5357 Evaluate side-chains 101 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 60 LYS 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 60 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.111970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096120 restraints weight = 6373.229| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.21 r_work: 0.3389 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5050 Z= 0.221 Angle : 0.515 6.976 6810 Z= 0.289 Chirality : 0.053 0.132 910 Planarity : 0.002 0.009 830 Dihedral : 5.436 22.545 720 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 6.08 % Allowed : 26.47 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.72 (0.28), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.011 0.002 PHE C 94 HIS 0.004 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5050) covalent geometry : angle 0.51527 ( 6810) hydrogen bonds : bond 0.02974 ( 166) hydrogen bonds : angle 5.11936 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.121 Fit side-chains REVERT: A 34 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7653 (mtpt) REVERT: A 43 LYS cc_start: 0.8573 (tttt) cc_final: 0.8309 (tttm) REVERT: A 60 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7403 (mtpp) REVERT: D 45 LYS cc_start: 0.7916 (mtpm) cc_final: 0.7392 (ttmm) REVERT: D 60 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.5711 (mptp) REVERT: E 45 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7377 (tppt) REVERT: E 60 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7181 (ttmp) REVERT: F 43 LYS cc_start: 0.8375 (tttt) cc_final: 0.8006 (tttm) REVERT: F 46 GLU cc_start: 0.8156 (tt0) cc_final: 0.7407 (tm-30) REVERT: F 60 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.6996 (mptt) REVERT: G 60 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6399 (mptt) REVERT: H 43 LYS cc_start: 0.8018 (tttt) cc_final: 0.7651 (tttm) REVERT: H 60 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.5841 (mptp) REVERT: I 60 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6382 (mptt) REVERT: J 45 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7424 (ttpt) outliers start: 31 outliers final: 19 residues processed: 105 average time/residue: 0.4843 time to fit residues: 53.1568 Evaluate side-chains 105 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 60 LYS 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 60 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN J 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089824 restraints weight = 6822.974| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.03 r_work: 0.3295 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.047 5050 Z= 0.473 Angle : 0.649 7.521 6810 Z= 0.373 Chirality : 0.060 0.157 910 Planarity : 0.003 0.010 830 Dihedral : 5.815 22.568 720 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 8.04 % Allowed : 25.88 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.020 0.004 PHE E 94 HIS 0.008 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00997 ( 5050) covalent geometry : angle 0.64931 ( 6810) hydrogen bonds : bond 0.03860 ( 166) hydrogen bonds : angle 5.53782 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.195 Fit side-chains REVERT: A 20 GLU cc_start: 0.7962 (mp0) cc_final: 0.7376 (mp0) REVERT: A 60 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7702 (mtpp) REVERT: B 35 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: D 60 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7101 (ttmm) REVERT: E 45 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7667 (tppt) REVERT: E 60 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6575 (mppt) REVERT: F 43 LYS cc_start: 0.8490 (tttt) cc_final: 0.8132 (tttm) REVERT: F 60 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7130 (mptp) REVERT: G 60 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6621 (mptt) REVERT: H 43 LYS cc_start: 0.8185 (tttt) cc_final: 0.7818 (tttp) REVERT: H 60 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6359 (mppt) REVERT: I 60 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6576 (mptt) REVERT: J 43 LYS cc_start: 0.8273 (tttt) cc_final: 0.7972 (tttp) outliers start: 41 outliers final: 26 residues processed: 105 average time/residue: 0.4934 time to fit residues: 54.2394 Evaluate side-chains 109 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 92 THR 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 60 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103978 restraints weight = 6067.790| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.05 r_work: 0.3491 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5050 Z= 0.121 Angle : 0.452 6.486 6810 Z= 0.250 Chirality : 0.051 0.127 910 Planarity : 0.002 0.009 830 Dihedral : 4.994 20.158 720 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.88 % Allowed : 27.84 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR G 39 PHE 0.007 0.001 PHE C 94 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5050) covalent geometry : angle 0.45219 ( 6810) hydrogen bonds : bond 0.02369 ( 166) hydrogen bonds : angle 4.99054 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.202 Fit side-chains REVERT: A 20 GLU cc_start: 0.7879 (mp0) cc_final: 0.7107 (tt0) REVERT: A 34 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7741 (mtpt) REVERT: B 43 LYS cc_start: 0.8641 (tttt) cc_final: 0.8361 (tttp) REVERT: B 44 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8571 (m) REVERT: E 45 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7406 (tppt) REVERT: F 43 LYS cc_start: 0.8454 (tttt) cc_final: 0.8130 (tttm) REVERT: F 60 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.6933 (mptp) REVERT: G 60 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6478 (mptt) REVERT: H 43 LYS cc_start: 0.8123 (tttt) cc_final: 0.7756 (tttm) REVERT: I 60 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6366 (mptt) REVERT: J 45 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7275 (ttpt) outliers start: 30 outliers final: 16 residues processed: 102 average time/residue: 0.4811 time to fit residues: 51.4930 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR 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 F residue 15 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.0030 chunk 52 optimal weight: 8.9990 overall best weight: 6.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 79 GLN I 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090635 restraints weight = 6939.686| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.07 r_work: 0.3317 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 5050 Z= 0.396 Angle : 0.599 7.411 6810 Z= 0.341 Chirality : 0.057 0.141 910 Planarity : 0.003 0.010 830 Dihedral : 5.515 22.240 720 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 7.84 % Allowed : 27.45 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 39 PHE 0.018 0.003 PHE E 94 HIS 0.006 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00832 ( 5050) covalent geometry : angle 0.59877 ( 6810) hydrogen bonds : bond 0.03510 ( 166) hydrogen bonds : angle 5.31542 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.167 Fit side-chains REVERT: A 20 GLU cc_start: 0.7934 (mp0) cc_final: 0.7257 (tt0) REVERT: A 60 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7524 (mtpp) REVERT: B 35 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: C 20 GLU cc_start: 0.7886 (mp0) cc_final: 0.7268 (mp0) REVERT: D 34 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7747 (mttt) REVERT: D 60 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7252 (tttt) REVERT: E 45 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7565 (tppt) REVERT: F 43 LYS cc_start: 0.8486 (tttt) cc_final: 0.8151 (tttm) REVERT: F 60 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7055 (mptp) REVERT: G 60 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6554 (mptt) REVERT: H 43 LYS cc_start: 0.8192 (tttt) cc_final: 0.7826 (tttp) REVERT: H 60 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6780 (ttmm) REVERT: I 60 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6598 (mptt) REVERT: J 43 LYS cc_start: 0.8206 (tttt) cc_final: 0.7914 (tttm) outliers start: 40 outliers final: 27 residues processed: 106 average time/residue: 0.4815 time to fit residues: 53.3993 Evaluate side-chains 112 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 92 THR 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 F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098361 restraints weight = 6153.868| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.07 r_work: 0.3406 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5050 Z= 0.214 Angle : 0.497 6.814 6810 Z= 0.277 Chirality : 0.052 0.130 910 Planarity : 0.002 0.010 830 Dihedral : 5.159 20.477 720 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 7.06 % Allowed : 27.84 % Favored : 65.10 % 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: -2.65 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR G 39 PHE 0.010 0.002 PHE E 94 HIS 0.003 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 5050) covalent geometry : angle 0.49665 ( 6810) hydrogen bonds : bond 0.02768 ( 166) hydrogen bonds : angle 4.99466 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.193 Fit side-chains REVERT: A 20 GLU cc_start: 0.7889 (mp0) cc_final: 0.7136 (tt0) REVERT: A 60 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7289 (mtpp) REVERT: B 35 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: B 44 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8498 (m) REVERT: B 60 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7213 (tppp) REVERT: E 45 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7487 (tppt) REVERT: F 43 LYS cc_start: 0.8435 (tttt) cc_final: 0.8110 (tttm) REVERT: F 60 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.6998 (mptp) REVERT: G 60 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6466 (mptt) REVERT: H 43 LYS cc_start: 0.8038 (tttt) cc_final: 0.7663 (tttm) REVERT: H 60 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6660 (ttmm) REVERT: I 60 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6321 (mptt) outliers start: 36 outliers final: 22 residues processed: 103 average time/residue: 0.4233 time to fit residues: 45.7853 Evaluate side-chains 105 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR 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 F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 79 GLN I 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095876 restraints weight = 6309.610| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.10 r_work: 0.3333 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 5050 Z= 0.280 Angle : 0.530 7.074 6810 Z= 0.299 Chirality : 0.053 0.131 910 Planarity : 0.002 0.010 830 Dihedral : 5.249 21.601 720 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.65 % Allowed : 26.47 % Favored : 65.88 % 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: -2.74 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.014 0.002 PHE E 94 HIS 0.004 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 5050) covalent geometry : angle 0.53020 ( 6810) hydrogen bonds : bond 0.03050 ( 166) hydrogen bonds : angle 5.05943 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.198 Fit side-chains REVERT: A 20 GLU cc_start: 0.7869 (mp0) cc_final: 0.7148 (tt0) REVERT: A 60 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7388 (mtpp) REVERT: B 35 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: B 44 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8494 (m) REVERT: B 60 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7204 (tttt) REVERT: C 20 GLU cc_start: 0.7928 (mp0) cc_final: 0.7240 (mp0) REVERT: C 35 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: D 34 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7484 (mttt) REVERT: E 45 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7451 (tppt) REVERT: F 43 LYS cc_start: 0.8384 (tttt) cc_final: 0.8042 (tttm) REVERT: F 60 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.6925 (mptp) REVERT: G 60 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6334 (mptt) REVERT: H 43 LYS cc_start: 0.8028 (tttt) cc_final: 0.7640 (tttm) REVERT: H 60 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6563 (ttmm) REVERT: I 60 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6427 (mptt) REVERT: J 43 LYS cc_start: 0.8111 (tttt) cc_final: 0.7801 (tttp) outliers start: 39 outliers final: 27 residues processed: 102 average time/residue: 0.4947 time to fit residues: 52.7966 Evaluate side-chains 112 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR 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 F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096161 restraints weight = 6173.954| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.07 r_work: 0.3339 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 5050 Z= 0.279 Angle : 0.528 7.107 6810 Z= 0.298 Chirality : 0.053 0.129 910 Planarity : 0.002 0.010 830 Dihedral : 5.236 21.659 720 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 7.25 % Allowed : 27.06 % Favored : 65.69 % 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: -2.80 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 PHE 0.013 0.002 PHE E 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 5050) covalent geometry : angle 0.52834 ( 6810) hydrogen bonds : bond 0.02987 ( 166) hydrogen bonds : angle 5.02346 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.201 Fit side-chains REVERT: A 20 GLU cc_start: 0.7857 (mp0) cc_final: 0.7152 (tt0) REVERT: A 60 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7406 (mtpp) REVERT: B 35 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: B 44 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 60 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7169 (tttt) REVERT: C 20 GLU cc_start: 0.7909 (mp0) cc_final: 0.7231 (mp0) REVERT: C 35 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: D 34 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7471 (mttt) REVERT: E 45 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7458 (tppt) REVERT: F 43 LYS cc_start: 0.8389 (tttt) cc_final: 0.8054 (tttm) REVERT: F 60 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.6951 (mptp) REVERT: G 60 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6339 (mptt) REVERT: H 43 LYS cc_start: 0.8026 (tttt) cc_final: 0.7637 (tttm) REVERT: H 60 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6567 (ttmm) REVERT: I 60 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6425 (mptt) REVERT: J 43 LYS cc_start: 0.8108 (tttt) cc_final: 0.7797 (tttp) outliers start: 37 outliers final: 26 residues processed: 101 average time/residue: 0.4857 time to fit residues: 51.3606 Evaluate side-chains 111 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR 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 F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.116163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100856 restraints weight = 6109.066| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.04 r_work: 0.3441 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5050 Z= 0.156 Angle : 0.464 6.635 6810 Z= 0.257 Chirality : 0.051 0.128 910 Planarity : 0.002 0.009 830 Dihedral : 4.879 19.943 720 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.08 % Allowed : 28.04 % Favored : 65.88 % 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: -2.69 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR F 39 PHE 0.008 0.001 PHE D 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5050) covalent geometry : angle 0.46377 ( 6810) hydrogen bonds : bond 0.02402 ( 166) hydrogen bonds : angle 4.80756 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.201 Fit side-chains REVERT: A 20 GLU cc_start: 0.7877 (mp0) cc_final: 0.7188 (tt0) REVERT: A 60 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7253 (mtpp) REVERT: B 35 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: B 43 LYS cc_start: 0.8656 (tttt) cc_final: 0.8305 (tttp) REVERT: B 44 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 60 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7242 (tppp) REVERT: C 35 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: E 45 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7471 (tppt) REVERT: F 43 LYS cc_start: 0.8461 (tttt) cc_final: 0.8167 (tttm) REVERT: G 60 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6417 (mptt) REVERT: H 43 LYS cc_start: 0.8062 (tttt) cc_final: 0.7687 (tttp) REVERT: H 60 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6727 (ttmm) REVERT: I 60 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6365 (mptt) REVERT: J 35 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7676 (mt-10) outliers start: 31 outliers final: 21 residues processed: 99 average time/residue: 0.4868 time to fit residues: 50.4960 Evaluate side-chains 101 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 79 GLN I 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089688 restraints weight = 7037.838| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.17 r_work: 0.3303 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 5050 Z= 0.389 Angle : 0.589 7.393 6810 Z= 0.336 Chirality : 0.057 0.149 910 Planarity : 0.002 0.010 830 Dihedral : 5.376 22.888 720 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 6.67 % Allowed : 28.04 % Favored : 65.29 % 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: -2.86 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.017 0.003 PHE E 94 HIS 0.006 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00817 ( 5050) covalent geometry : angle 0.58924 ( 6810) hydrogen bonds : bond 0.03291 ( 166) hydrogen bonds : angle 5.14035 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.21 seconds wall clock time: 31 minutes 9.11 seconds (1869.11 seconds total)