Starting phenix.real_space_refine on Wed Mar 4 05:38:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh7_14726/03_2026/7zh7_14726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh7_14726/03_2026/7zh7_14726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zh7_14726/03_2026/7zh7_14726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh7_14726/03_2026/7zh7_14726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zh7_14726/03_2026/7zh7_14726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh7_14726/03_2026/7zh7_14726.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3830 2.51 5 N 1140 2.21 5 O 1140 1.98 5 H 5390 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11520 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "D" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "F" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "H" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "I" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Chain: "J" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1152 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'TRANS': 74} Time building chain proxies: 2.30, per 1000 atoms: 0.20 Number of scatterers: 11520 At special positions: 0 Unit cell: (118.237, 91.567, 52.451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1140 8.00 N 1140 7.00 C 3830 6.00 H 5390 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 385.1 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 20 through 28 removed outlier: 9.084A pdb=" N TRP B 20 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N PHE D 23 " --> pdb=" O TRP B 20 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER B 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLY D 25 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ALA D 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 26 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N TRP A 20 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N PHE B 23 " --> pdb=" O TRP A 20 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER A 22 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N GLY B 25 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU A 24 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ALA B 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A 26 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR A 21 " --> pdb=" O TRP C 20 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER C 22 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE A 23 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR C 21 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER E 22 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE C 23 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 25 " --> pdb=" O LEU E 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 40 removed outlier: 5.949A pdb=" N ALA B 37 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP D 40 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER B 39 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA A 37 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP B 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 39 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA C 37 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA E 37 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 47 removed outlier: 6.452A pdb=" N TYR A 46 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR C 46 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 56 removed outlier: 7.052A pdb=" N LYS B 51 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR D 52 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 53 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 51 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR B 52 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 53 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ASP A 50 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N PHE C 53 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 52 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ALA C 55 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS A 54 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASP C 50 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N PHE E 53 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR C 52 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ALA E 55 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 54 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.610A pdb=" N GLN A 63 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN C 63 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 79 removed outlier: 7.032A pdb=" N TRP D 70 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA B 71 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA D 72 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS B 73 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL D 74 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 75 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER D 76 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TRP B 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 71 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA B 72 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS A 73 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 74 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 76 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N TRP A 70 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N LYS C 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ALA A 72 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N ILE C 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL A 74 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N ASP C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER A 76 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ARG C 79 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 78 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N TRP C 70 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LYS E 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ALA C 72 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ILE E 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL C 74 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N ASP E 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER C 76 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ARG E 79 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 78 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 90 removed outlier: 8.803A pdb=" N SER B 82 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N VAL D 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ARG B 84 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ASP D 87 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR B 86 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE D 89 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 88 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N SER A 82 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N VAL B 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ARG A 84 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N ASP B 87 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N THR A 86 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE B 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE A 88 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN A 83 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG C 84 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 85 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR C 86 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP A 87 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN C 83 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG E 84 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 85 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR E 86 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP C 87 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 20 through 28 removed outlier: 9.088A pdb=" N TRP G 20 " --> pdb=" O TYR I 21 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N PHE I 23 " --> pdb=" O TRP G 20 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER G 22 " --> pdb=" O PHE I 23 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N GLY I 25 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA I 27 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU G 26 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N TRP F 20 " --> pdb=" O TYR G 21 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N PHE G 23 " --> pdb=" O TRP F 20 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER F 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N GLY G 25 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU F 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ALA G 27 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU F 26 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR F 21 " --> pdb=" O TRP H 20 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER H 22 " --> pdb=" O TYR F 21 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE F 23 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR H 21 " --> pdb=" O TRP J 20 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER J 22 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE H 23 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY H 25 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 36 through 40 removed outlier: 5.957A pdb=" N ALA G 37 " --> pdb=" O TYR I 38 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP I 40 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER G 39 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA F 37 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP G 40 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER F 39 " --> pdb=" O ASP G 40 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA H 37 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA J 37 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 45 through 47 removed outlier: 6.449A pdb=" N TYR F 46 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR H 46 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 50 through 56 removed outlier: 7.036A pdb=" N LYS G 51 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR I 52 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 53 " --> pdb=" O TYR I 52 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS F 51 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR G 52 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE F 53 " --> pdb=" O TYR G 52 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ASP F 50 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N PHE H 53 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR F 52 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ALA H 55 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS F 54 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ASP H 50 " --> pdb=" O LYS J 51 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N PHE J 53 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR H 52 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ALA J 55 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS H 54 " --> pdb=" O ALA J 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 63 through 64 removed outlier: 6.614A pdb=" N GLN F 63 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN H 63 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 69 through 79 removed outlier: 7.031A pdb=" N TRP I 70 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA G 71 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA I 72 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS G 73 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL I 74 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE G 75 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER I 76 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TRP G 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA F 71 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA G 72 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS F 73 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL G 74 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE F 75 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER G 76 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N TRP F 70 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N LYS H 73 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ALA F 72 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N ILE H 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N VAL F 74 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N ASP H 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER F 76 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG H 79 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA F 78 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N TRP H 70 " --> pdb=" O ALA J 71 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N LYS J 73 " --> pdb=" O TRP H 70 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N ALA H 72 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ILE J 75 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N VAL H 74 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ASP J 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER H 76 " --> pdb=" O ASP J 77 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ARG J 79 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA H 78 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 82 through 90 removed outlier: 8.803A pdb=" N SER G 82 " --> pdb=" O GLN I 83 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N VAL I 85 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ARG G 84 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N ASP I 87 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR G 86 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE I 89 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE G 88 " --> pdb=" O PHE I 89 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N SER F 82 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N VAL G 85 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ARG F 84 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ASP G 87 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR F 86 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N PHE G 89 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE F 88 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN F 83 " --> pdb=" O SER H 82 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG H 84 " --> pdb=" O GLN F 83 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL F 85 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR H 86 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP F 87 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN H 83 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG J 84 " --> pdb=" O GLN H 83 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL H 85 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR J 86 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP H 87 " --> pdb=" O THR J 86 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 234 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: 2.35 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5390 1.03 - 1.22: 0 1.22 - 1.42: 3157 1.42 - 1.61: 3123 1.61 - 1.80: 40 Bond restraints: 11710 Sorted by residual: bond pdb=" CG PRO G 66 " pdb=" CD PRO G 66 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.32e+00 bond pdb=" CG PRO J 66 " pdb=" CD PRO J 66 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.32e+00 bond pdb=" CG PRO C 66 " pdb=" CD PRO C 66 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.31e+00 bond pdb=" CG PRO I 66 " pdb=" CD PRO I 66 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.29e+00 bond pdb=" CG PRO D 66 " pdb=" CD PRO D 66 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.26e+00 ... (remaining 11705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 18970 1.09 - 2.18: 1415 2.18 - 3.26: 180 3.26 - 4.35: 30 4.35 - 5.44: 15 Bond angle restraints: 20610 Sorted by residual: angle pdb=" N ASN B 45 " pdb=" CA ASN B 45 " pdb=" C ASN B 45 " ideal model delta sigma weight residual 107.48 112.92 -5.44 2.29e+00 1.91e-01 5.64e+00 angle pdb=" N ASN G 45 " pdb=" CA ASN G 45 " pdb=" C ASN G 45 " ideal model delta sigma weight residual 107.48 112.88 -5.40 2.29e+00 1.91e-01 5.56e+00 angle pdb=" N ASN F 45 " pdb=" CA ASN F 45 " pdb=" C ASN F 45 " ideal model delta sigma weight residual 107.48 112.84 -5.36 2.29e+00 1.91e-01 5.47e+00 angle pdb=" N ASN H 45 " pdb=" CA ASN H 45 " pdb=" C ASN H 45 " ideal model delta sigma weight residual 107.48 112.82 -5.34 2.29e+00 1.91e-01 5.43e+00 angle pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" C ASN A 45 " ideal model delta sigma weight residual 107.48 112.79 -5.31 2.29e+00 1.91e-01 5.38e+00 ... (remaining 20605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 4951 12.00 - 24.00: 372 24.00 - 36.00: 137 36.00 - 47.99: 80 47.99 - 59.99: 70 Dihedral angle restraints: 5610 sinusoidal: 2750 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ALA E 44 " pdb=" C ALA E 44 " pdb=" N ASN E 45 " pdb=" CA ASN E 45 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA H 44 " pdb=" C ALA H 44 " pdb=" N ASN H 45 " pdb=" CA ASN H 45 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA B 44 " pdb=" C ALA B 44 " pdb=" N ASN B 45 " pdb=" CA ASN B 45 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 306 0.029 - 0.058: 310 0.058 - 0.087: 72 0.087 - 0.116: 22 0.116 - 0.145: 30 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE G 75 " pdb=" N ILE G 75 " pdb=" C ILE G 75 " pdb=" CB ILE G 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 737 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 36 " -0.231 9.50e-02 1.11e+02 7.76e-02 7.59e+00 pdb=" NE ARG A 36 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 36 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 36 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 36 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 36 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 36 " -0.003 2.00e-02 2.50e+03 pdb="HH21 ARG A 36 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 36 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 36 " -0.233 9.50e-02 1.11e+02 7.83e-02 7.58e+00 pdb=" NE ARG I 36 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG I 36 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 36 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG I 36 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG I 36 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG I 36 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG I 36 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG I 36 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 36 " -0.233 9.50e-02 1.11e+02 7.81e-02 7.57e+00 pdb=" NE ARG B 36 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 36 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 36 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 36 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG B 36 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B 36 " -0.003 2.00e-02 2.50e+03 pdb="HH21 ARG B 36 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 36 " -0.006 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 2802 2.32 - 2.89: 24310 2.89 - 3.46: 25691 3.46 - 4.03: 40545 4.03 - 4.60: 57799 Nonbonded interactions: 151147 Sorted by model distance: nonbonded pdb="HH21 ARG F 90 " pdb=" OE2 GLU I 19 " model vdw 1.755 2.450 nonbonded pdb="HH21 ARG A 90 " pdb=" OE2 GLU D 19 " model vdw 1.762 2.450 nonbonded pdb="HH11 ARG F 64 " pdb=" OH TYR G 59 " model vdw 1.855 2.450 nonbonded pdb="HH11 ARG G 64 " pdb=" OH TYR I 59 " model vdw 1.857 2.450 nonbonded pdb="HH11 ARG A 64 " pdb=" OH TYR B 59 " model vdw 1.857 2.450 ... (remaining 151142 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: 0.01 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: 1.030 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: 0.050 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.003 0.031 6320 Z= 0.129 Angle : 0.737 5.439 8530 Z= 0.424 Chirality : 0.048 0.145 740 Planarity : 0.011 0.100 1150 Dihedral : 11.414 57.823 2170 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.42 (0.17), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.13), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 36 TYR 0.014 0.004 TYR J 21 PHE 0.014 0.003 PHE E 88 TRP 0.020 0.005 TRP J 35 HIS 0.001 0.000 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6320) covalent geometry : angle 0.73681 ( 8530) hydrogen bonds : bond 0.23362 ( 78) hydrogen bonds : angle 12.28946 ( 234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6448 (ttp-170) REVERT: B 73 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7982 (mtmm) REVERT: D 21 TYR cc_start: 0.7730 (m-10) cc_final: 0.7404 (m-10) REVERT: D 42 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.6253 (mmp-170) REVERT: D 73 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7207 (mttm) REVERT: E 73 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7288 (pttp) REVERT: F 56 ARG cc_start: 0.7023 (ttt180) cc_final: 0.6467 (ttp-170) REVERT: G 73 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7981 (mtmm) REVERT: I 21 TYR cc_start: 0.7733 (m-10) cc_final: 0.7452 (m-10) REVERT: I 42 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.6262 (mmp-170) REVERT: I 73 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7222 (mttm) REVERT: J 73 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7317 (pttp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3527 time to fit residues: 77.3367 Evaluate side-chains 146 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 54 HIS D 54 HIS E 54 HIS F 54 HIS F 91 HIS G 54 HIS I 54 HIS J 54 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.200944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.187691 restraints weight = 21650.799| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.16 r_work: 0.4293 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6320 Z= 0.142 Angle : 0.555 5.936 8530 Z= 0.320 Chirality : 0.047 0.138 740 Planarity : 0.003 0.028 1150 Dihedral : 5.724 18.759 870 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.18 % Allowed : 7.82 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.24 (0.18), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.14), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 79 TYR 0.009 0.001 TYR F 21 PHE 0.013 0.001 PHE J 23 TRP 0.010 0.001 TRP H 20 HIS 0.008 0.002 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6320) covalent geometry : angle 0.55468 ( 8530) hydrogen bonds : bond 0.03539 ( 78) hydrogen bonds : angle 7.72648 ( 234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6608 (ttp-170) REVERT: A 87 ASP cc_start: 0.8006 (m-30) cc_final: 0.7737 (m-30) REVERT: C 87 ASP cc_start: 0.8169 (m-30) cc_final: 0.7921 (m-30) REVERT: D 42 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.6336 (mmp-170) REVERT: D 73 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7364 (mttm) REVERT: E 73 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7449 (pttp) REVERT: F 43 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7412 (mt-10) REVERT: F 46 TYR cc_start: 0.7972 (m-10) cc_final: 0.7466 (m-10) REVERT: F 56 ARG cc_start: 0.7261 (ttt180) cc_final: 0.6625 (ttp-170) REVERT: H 87 ASP cc_start: 0.8138 (m-30) cc_final: 0.7927 (m-30) REVERT: I 42 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.6322 (mmp-170) REVERT: I 73 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7345 (mttm) REVERT: J 73 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7456 (pttp) outliers start: 12 outliers final: 5 residues processed: 159 average time/residue: 0.3378 time to fit residues: 61.9894 Evaluate side-chains 127 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS E 54 HIS F 54 HIS G 54 HIS H 54 HIS J 54 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.190342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.177141 restraints weight = 22216.260| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.17 r_work: 0.4350 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4255 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6320 Z= 0.269 Angle : 0.660 5.834 8530 Z= 0.382 Chirality : 0.050 0.154 740 Planarity : 0.004 0.033 1150 Dihedral : 6.170 19.792 870 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.64 % Allowed : 9.27 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.52 (0.19), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.14), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 90 TYR 0.018 0.002 TYR A 21 PHE 0.014 0.002 PHE E 23 TRP 0.011 0.002 TRP F 20 HIS 0.017 0.002 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 6320) covalent geometry : angle 0.66001 ( 8530) hydrogen bonds : bond 0.05097 ( 78) hydrogen bonds : angle 8.22075 ( 234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7569 (mt-10) REVERT: A 87 ASP cc_start: 0.8114 (m-30) cc_final: 0.7888 (m-30) REVERT: C 87 ASP cc_start: 0.8116 (m-30) cc_final: 0.7905 (m-30) REVERT: D 42 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.6511 (mmp-170) REVERT: D 73 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7539 (mttm) REVERT: E 73 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7487 (pttp) REVERT: F 43 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7566 (mt-10) REVERT: G 87 ASP cc_start: 0.8221 (m-30) cc_final: 0.7983 (m-30) REVERT: I 42 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.6434 (mmp-170) REVERT: I 46 TYR cc_start: 0.7848 (m-10) cc_final: 0.7543 (m-10) REVERT: I 73 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7477 (mttm) REVERT: J 73 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7506 (pttp) outliers start: 9 outliers final: 4 residues processed: 132 average time/residue: 0.3688 time to fit residues: 55.8100 Evaluate side-chains 112 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 HIS F 54 HIS J 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.191961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.178856 restraints weight = 22227.249| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.17 r_work: 0.4227 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6320 Z= 0.168 Angle : 0.546 4.952 8530 Z= 0.317 Chirality : 0.047 0.137 740 Planarity : 0.003 0.026 1150 Dihedral : 5.848 18.104 870 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.27 % Allowed : 10.00 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.41 (0.20), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.15), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 36 TYR 0.015 0.001 TYR A 46 PHE 0.008 0.002 PHE J 23 TRP 0.009 0.001 TRP A 35 HIS 0.005 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6320) covalent geometry : angle 0.54586 ( 8530) hydrogen bonds : bond 0.03721 ( 78) hydrogen bonds : angle 7.71471 ( 234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 87 ASP cc_start: 0.8030 (m-30) cc_final: 0.7769 (m-30) REVERT: C 87 ASP cc_start: 0.8087 (m-30) cc_final: 0.7790 (m-30) REVERT: D 42 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.6395 (mmp-170) REVERT: D 73 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7461 (mttm) REVERT: E 73 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7492 (pttp) REVERT: F 46 TYR cc_start: 0.8107 (m-10) cc_final: 0.7843 (m-10) REVERT: I 42 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.6382 (mmp-170) REVERT: I 73 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7445 (mttm) REVERT: J 73 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7486 (pttp) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.3255 time to fit residues: 46.5351 Evaluate side-chains 112 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain J residue 43 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.190457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.177500 restraints weight = 22124.495| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.14 r_work: 0.4194 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6320 Z= 0.189 Angle : 0.551 5.628 8530 Z= 0.321 Chirality : 0.047 0.138 740 Planarity : 0.003 0.026 1150 Dihedral : 5.801 19.012 870 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.64 % Allowed : 11.82 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.43 (0.21), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 36 TYR 0.019 0.001 TYR A 46 PHE 0.011 0.002 PHE E 23 TRP 0.010 0.002 TRP A 35 HIS 0.005 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6320) covalent geometry : angle 0.55091 ( 8530) hydrogen bonds : bond 0.03872 ( 78) hydrogen bonds : angle 7.65259 ( 234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 47 ILE cc_start: 0.8047 (mt) cc_final: 0.7783 (mm) REVERT: A 87 ASP cc_start: 0.7996 (m-30) cc_final: 0.7768 (m-30) REVERT: C 87 ASP cc_start: 0.8118 (m-30) cc_final: 0.7800 (m-30) REVERT: D 42 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.6402 (mmp-170) REVERT: D 73 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7460 (mttm) REVERT: E 73 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7532 (pttp) REVERT: F 43 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7165 (mt-10) REVERT: F 46 TYR cc_start: 0.8037 (m-10) cc_final: 0.7592 (m-10) REVERT: I 42 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.6366 (mmp-170) REVERT: I 73 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7464 (mttm) REVERT: J 73 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7555 (pttp) outliers start: 9 outliers final: 7 residues processed: 124 average time/residue: 0.3197 time to fit residues: 46.1993 Evaluate side-chains 115 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.185012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.172076 restraints weight = 22444.626| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.11 r_work: 0.4138 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4041 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 6320 Z= 0.312 Angle : 0.666 5.530 8530 Z= 0.388 Chirality : 0.051 0.148 740 Planarity : 0.005 0.033 1150 Dihedral : 6.264 19.788 870 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 2.36 % Allowed : 13.64 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.60 (0.20), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 90 TYR 0.019 0.002 TYR A 46 PHE 0.013 0.002 PHE A 88 TRP 0.013 0.002 TRP D 70 HIS 0.005 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00729 ( 6320) covalent geometry : angle 0.66603 ( 8530) hydrogen bonds : bond 0.04961 ( 78) hydrogen bonds : angle 7.92059 ( 234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 87 ASP cc_start: 0.8149 (m-30) cc_final: 0.7861 (m-30) REVERT: B 41 MET cc_start: 0.8305 (mtt) cc_final: 0.8028 (mtt) REVERT: C 87 ASP cc_start: 0.8152 (m-30) cc_final: 0.7845 (m-30) REVERT: D 42 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.6434 (mmp-170) REVERT: D 46 TYR cc_start: 0.7814 (m-10) cc_final: 0.7371 (m-10) REVERT: D 47 ILE cc_start: 0.8150 (mt) cc_final: 0.7942 (mm) REVERT: D 73 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7420 (mttm) REVERT: E 73 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7534 (pttp) REVERT: F 43 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7350 (mt-10) REVERT: F 46 TYR cc_start: 0.8203 (m-10) cc_final: 0.7875 (m-10) REVERT: G 41 MET cc_start: 0.8298 (mtt) cc_final: 0.7987 (mtt) REVERT: I 42 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.6451 (mmp-170) REVERT: I 46 TYR cc_start: 0.7664 (m-10) cc_final: 0.7206 (m-10) REVERT: I 73 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7452 (mttm) REVERT: J 73 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7517 (pttp) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.2929 time to fit residues: 42.7762 Evaluate side-chains 114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 43 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.187584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.174744 restraints weight = 22510.102| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.10 r_work: 0.4290 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6320 Z= 0.219 Angle : 0.586 4.796 8530 Z= 0.341 Chirality : 0.048 0.141 740 Planarity : 0.004 0.027 1150 Dihedral : 5.995 19.088 870 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.18 % Allowed : 14.18 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.53 (0.21), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 36 TYR 0.015 0.002 TYR A 46 PHE 0.010 0.002 PHE E 23 TRP 0.010 0.002 TRP F 70 HIS 0.005 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 6320) covalent geometry : angle 0.58624 ( 8530) hydrogen bonds : bond 0.04178 ( 78) hydrogen bonds : angle 7.74613 ( 234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 87 ASP cc_start: 0.8028 (m-30) cc_final: 0.7738 (m-30) REVERT: B 41 MET cc_start: 0.8305 (mtt) cc_final: 0.8048 (mtt) REVERT: C 87 ASP cc_start: 0.8092 (m-30) cc_final: 0.7776 (m-30) REVERT: D 42 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.6548 (mmp-170) REVERT: D 46 TYR cc_start: 0.7648 (m-10) cc_final: 0.7322 (m-10) REVERT: D 73 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7539 (mttm) REVERT: E 73 LYS cc_start: 0.8441 (mtmt) cc_final: 0.7596 (pttp) REVERT: F 43 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7434 (mt-10) REVERT: F 46 TYR cc_start: 0.8114 (m-10) cc_final: 0.7827 (m-10) REVERT: G 41 MET cc_start: 0.8291 (mtt) cc_final: 0.8030 (mtt) REVERT: I 42 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.6546 (mmp-170) REVERT: I 46 TYR cc_start: 0.7660 (m-10) cc_final: 0.7353 (m-10) REVERT: I 73 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7516 (mttm) REVERT: J 73 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7582 (pttp) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.2995 time to fit residues: 39.8980 Evaluate side-chains 107 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 43 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 58 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 HIS J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.191883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.179284 restraints weight = 22396.084| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.04 r_work: 0.4330 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4237 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6320 Z= 0.152 Angle : 0.524 3.995 8530 Z= 0.306 Chirality : 0.046 0.135 740 Planarity : 0.003 0.025 1150 Dihedral : 5.697 19.762 870 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.82 % Allowed : 15.27 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.45 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.016 0.001 TYR A 46 PHE 0.010 0.002 PHE A 88 TRP 0.007 0.001 TRP A 70 HIS 0.006 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6320) covalent geometry : angle 0.52381 ( 8530) hydrogen bonds : bond 0.03469 ( 78) hydrogen bonds : angle 7.27543 ( 234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 87 ASP cc_start: 0.8068 (m-30) cc_final: 0.7768 (m-30) REVERT: B 41 MET cc_start: 0.8287 (mtt) cc_final: 0.7995 (mtt) REVERT: C 87 ASP cc_start: 0.8070 (m-30) cc_final: 0.7738 (m-30) REVERT: D 42 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.6550 (mmp-170) REVERT: D 46 TYR cc_start: 0.7550 (m-10) cc_final: 0.7283 (m-10) REVERT: D 73 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7518 (mttm) REVERT: E 73 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7556 (pttp) REVERT: F 43 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7312 (mt-10) REVERT: F 46 TYR cc_start: 0.8001 (m-10) cc_final: 0.7676 (m-10) REVERT: G 41 MET cc_start: 0.8239 (mtt) cc_final: 0.7920 (mtt) REVERT: I 42 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.6449 (mmp-170) REVERT: I 46 TYR cc_start: 0.7480 (m-10) cc_final: 0.7176 (m-10) REVERT: I 73 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7412 (mttm) REVERT: J 73 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7539 (pttp) outliers start: 10 outliers final: 8 residues processed: 109 average time/residue: 0.2924 time to fit residues: 37.5061 Evaluate side-chains 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain J residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS E 54 HIS J 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.188734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.175944 restraints weight = 22391.200| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.10 r_work: 0.4190 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6320 Z= 0.195 Angle : 0.556 5.362 8530 Z= 0.324 Chirality : 0.047 0.142 740 Planarity : 0.003 0.024 1150 Dihedral : 5.775 19.591 870 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 1.64 % Allowed : 15.27 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.48 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 90 TYR 0.020 0.002 TYR A 46 PHE 0.010 0.002 PHE A 88 TRP 0.009 0.001 TRP F 70 HIS 0.006 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6320) covalent geometry : angle 0.55561 ( 8530) hydrogen bonds : bond 0.03803 ( 78) hydrogen bonds : angle 7.28733 ( 234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 87 ASP cc_start: 0.8110 (m-30) cc_final: 0.7842 (m-30) REVERT: B 41 MET cc_start: 0.8315 (mtt) cc_final: 0.7978 (mtt) REVERT: C 87 ASP cc_start: 0.8097 (m-30) cc_final: 0.7764 (m-30) REVERT: D 42 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.6497 (mmp-170) REVERT: D 46 TYR cc_start: 0.7604 (m-10) cc_final: 0.7313 (m-10) REVERT: D 73 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7488 (mttm) REVERT: E 73 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7545 (pttp) REVERT: F 43 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7264 (mt-10) REVERT: F 46 TYR cc_start: 0.8061 (m-10) cc_final: 0.7717 (m-10) REVERT: G 41 MET cc_start: 0.8289 (mtt) cc_final: 0.7939 (mtt) REVERT: I 42 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.6466 (mmp-170) REVERT: I 46 TYR cc_start: 0.7541 (m-10) cc_final: 0.7267 (m-10) REVERT: I 73 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7374 (mttm) REVERT: J 73 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7527 (pttp) outliers start: 9 outliers final: 7 residues processed: 105 average time/residue: 0.2630 time to fit residues: 32.9245 Evaluate side-chains 105 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain J residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 HIS J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.189228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.176339 restraints weight = 22576.360| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.12 r_work: 0.4289 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6320 Z= 0.179 Angle : 0.543 5.394 8530 Z= 0.316 Chirality : 0.047 0.139 740 Planarity : 0.003 0.024 1150 Dihedral : 5.720 19.340 870 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 1.64 % Allowed : 15.09 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.44 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 36 TYR 0.020 0.002 TYR A 46 PHE 0.009 0.002 PHE A 23 TRP 0.008 0.001 TRP A 70 HIS 0.007 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6320) covalent geometry : angle 0.54297 ( 8530) hydrogen bonds : bond 0.03645 ( 78) hydrogen bonds : angle 7.17449 ( 234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7516 (mt-10) REVERT: A 87 ASP cc_start: 0.8095 (m-30) cc_final: 0.7828 (m-30) REVERT: B 41 MET cc_start: 0.8319 (mtt) cc_final: 0.7992 (mtt) REVERT: C 87 ASP cc_start: 0.8093 (m-30) cc_final: 0.7774 (m-30) REVERT: D 42 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.6556 (mmp-170) REVERT: D 46 TYR cc_start: 0.7549 (m-10) cc_final: 0.7275 (m-10) REVERT: D 73 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7529 (mttm) REVERT: E 42 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8190 (mtt180) REVERT: E 73 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7557 (pttp) REVERT: F 43 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7267 (mt-10) REVERT: F 46 TYR cc_start: 0.8023 (m-10) cc_final: 0.7671 (m-10) REVERT: G 41 MET cc_start: 0.8319 (mtt) cc_final: 0.7979 (mtt) REVERT: I 42 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.6519 (mmp-170) REVERT: I 46 TYR cc_start: 0.7503 (m-10) cc_final: 0.7204 (m-10) REVERT: I 73 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7471 (mttm) REVERT: J 42 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8183 (mtt180) REVERT: J 73 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7519 (pttp) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.2655 time to fit residues: 32.6908 Evaluate side-chains 104 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain J residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 HIS F 45 ASN J 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.185813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.172896 restraints weight = 22596.135| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.10 r_work: 0.4249 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6320 Z= 0.267 Angle : 0.620 5.875 8530 Z= 0.361 Chirality : 0.050 0.147 740 Planarity : 0.004 0.026 1150 Dihedral : 6.025 20.433 870 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -4.55 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 90 TYR 0.024 0.002 TYR A 46 PHE 0.012 0.002 PHE A 23 TRP 0.011 0.002 TRP A 70 HIS 0.006 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 6320) covalent geometry : angle 0.61988 ( 8530) hydrogen bonds : bond 0.04353 ( 78) hydrogen bonds : angle 7.46204 ( 234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2912.30 seconds wall clock time: 49 minutes 55.95 seconds (2995.95 seconds total)