Starting phenix.real_space_refine on Tue Jul 29 10:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh7_14726/07_2025/7zh7_14726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh7_14726/07_2025/7zh7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh7_14726/07_2025/7zh7_14726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh7_14726/07_2025/7zh7_14726.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh7_14726/07_2025/7zh7_14726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh7_14726/07_2025/7zh7_14726.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.56, per 1000 atoms: 0.57 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: 3.20 Conformation dependent library (CDL) restraints added in 854.0 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: 1.22 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: 3.74 Time building geometry restraints manager: 3.89 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.090 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.005 TRP J 35 HIS 0.001 0.000 HIS E 91 PHE 0.014 0.003 PHE E 88 TYR 0.014 0.004 TYR J 21 ARG 0.019 0.002 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.23362 ( 78) hydrogen bonds : angle 12.28946 ( 234) covalent geometry : bond 0.00276 ( 6320) covalent geometry : angle 0.73681 ( 8530) *********************** 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 : 0.865 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: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6449 (ttp-170) 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: 0.6252 (mmp-170) REVERT: D 73 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7168 (mttm) REVERT: E 73 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7284 (pttp) REVERT: F 56 ARG cc_start: 0.7023 (ttt180) cc_final: 0.6467 (ttp-170) REVERT: I 21 TYR cc_start: 0.7733 (m-10) cc_final: 0.7453 (m-10) REVERT: I 42 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.6261 (mmp-170) REVERT: I 73 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7185 (mttm) REVERT: J 73 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7312 (pttp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.7020 time to fit residues: 155.3614 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 : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS D 54 HIS ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS F 54 HIS ** F 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS H 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 = 0.4557 r_free = 0.4557 target = 0.192118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.179066 restraints weight = 21787.715| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.15 r_work: 0.4177 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 6320 Z= 0.292 Angle : 0.718 6.614 8530 Z= 0.415 Chirality : 0.052 0.156 740 Planarity : 0.005 0.032 1150 Dihedral : 6.330 21.679 870 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.00 % Allowed : 8.18 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.18), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.13), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 20 HIS 0.006 0.002 HIS E 54 PHE 0.015 0.002 PHE E 23 TYR 0.013 0.002 TYR I 21 ARG 0.006 0.001 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 78) hydrogen bonds : angle 8.21110 ( 234) covalent geometry : bond 0.00677 ( 6320) covalent geometry : angle 0.71813 ( 8530) *********************** 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 153 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.925 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: A 42 ARG cc_start: 0.8398 (mtt180) cc_final: 0.8102 (mtt180) REVERT: A 43 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7284 (mt-10) REVERT: A 46 TYR cc_start: 0.8124 (m-10) cc_final: 0.7619 (m-10) REVERT: A 56 ARG cc_start: 0.7383 (ttt180) cc_final: 0.6731 (ttp-170) REVERT: A 87 ASP cc_start: 0.8159 (m-30) cc_final: 0.7866 (m-30) REVERT: C 42 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8056 (mtt180) REVERT: C 87 ASP cc_start: 0.8217 (m-30) cc_final: 0.7978 (m-30) REVERT: D 42 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.6396 (mmp-170) REVERT: D 46 TYR cc_start: 0.8064 (m-10) cc_final: 0.7639 (m-10) REVERT: D 73 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7368 (mttm) REVERT: E 19 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7311 (mt-10) REVERT: E 34 MET cc_start: 0.8343 (mtt) cc_final: 0.8076 (mtt) REVERT: E 73 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7425 (pttp) REVERT: F 42 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8158 (mtt180) REVERT: F 43 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7539 (mt-10) REVERT: F 46 TYR cc_start: 0.8229 (m-10) cc_final: 0.7876 (m-10) REVERT: F 56 ARG cc_start: 0.7379 (ttt180) cc_final: 0.6740 (ttp-170) REVERT: F 87 ASP cc_start: 0.8184 (m-30) cc_final: 0.7909 (m-30) REVERT: H 42 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8078 (mtt180) REVERT: H 52 TYR cc_start: 0.8474 (m-80) cc_final: 0.8213 (m-80) REVERT: H 87 ASP cc_start: 0.8228 (m-30) cc_final: 0.7979 (m-30) REVERT: I 42 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.6353 (mmp-170) REVERT: I 46 TYR cc_start: 0.8070 (m-10) cc_final: 0.7636 (m-10) REVERT: I 73 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7321 (mttm) REVERT: J 19 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7319 (mt-10) REVERT: J 34 MET cc_start: 0.8396 (mtt) cc_final: 0.8138 (mtt) REVERT: J 73 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7428 (pttp) outliers start: 11 outliers final: 4 residues processed: 153 average time/residue: 0.7563 time to fit residues: 134.8781 Evaluate side-chains 132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS F 54 HIS F 91 HIS J 54 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.192957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.179884 restraints weight = 22117.172| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.14 r_work: 0.4210 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6320 Z= 0.219 Angle : 0.616 5.274 8530 Z= 0.354 Chirality : 0.048 0.142 740 Planarity : 0.004 0.028 1150 Dihedral : 6.141 21.312 870 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.09 % Allowed : 10.91 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.19), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.14), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 70 HIS 0.006 0.001 HIS J 54 PHE 0.012 0.002 PHE F 88 TYR 0.011 0.001 TYR A 21 ARG 0.004 0.001 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 78) hydrogen bonds : angle 7.94843 ( 234) covalent geometry : bond 0.00513 ( 6320) covalent geometry : angle 0.61627 ( 8530) *********************** 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: 6 poor density : 126 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8429 (mtt180) cc_final: 0.8202 (mtt180) REVERT: A 43 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7287 (mt-10) REVERT: A 46 TYR cc_start: 0.8141 (m-10) cc_final: 0.7731 (m-10) REVERT: C 42 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8168 (mtt180) REVERT: C 87 ASP cc_start: 0.8135 (m-30) cc_final: 0.7838 (m-30) REVERT: D 42 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.6389 (mmp-170) REVERT: D 46 TYR cc_start: 0.8032 (m-10) cc_final: 0.7702 (m-10) REVERT: D 73 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7363 (mttm) REVERT: E 19 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7331 (mt-10) REVERT: E 34 MET cc_start: 0.8357 (mtt) cc_final: 0.8049 (mtt) REVERT: E 73 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7507 (pttp) REVERT: F 43 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7356 (mt-10) REVERT: F 46 TYR cc_start: 0.8193 (m-10) cc_final: 0.7778 (m-10) REVERT: H 42 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8183 (mtt180) REVERT: H 52 TYR cc_start: 0.8687 (m-80) cc_final: 0.8476 (m-80) REVERT: H 87 ASP cc_start: 0.8151 (m-30) cc_final: 0.7856 (m-30) REVERT: I 42 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.6334 (mmp-170) REVERT: I 46 TYR cc_start: 0.7981 (m-10) cc_final: 0.7599 (m-10) REVERT: I 73 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7274 (mttm) REVERT: J 19 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7469 (mt-10) REVERT: J 34 MET cc_start: 0.8417 (mtt) cc_final: 0.8111 (mtt) REVERT: J 73 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7511 (pttp) outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.7896 time to fit residues: 119.8272 Evaluate side-chains 124 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 42 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.191939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.178646 restraints weight = 22179.876| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.17 r_work: 0.4217 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4114 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= 0.163 Angle : 0.530 4.307 8530 Z= 0.311 Chirality : 0.046 0.136 740 Planarity : 0.003 0.025 1150 Dihedral : 5.840 21.035 870 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.00 % Allowed : 10.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.20), 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 TRP 0.008 0.001 TRP C 35 HIS 0.006 0.001 HIS E 54 PHE 0.012 0.002 PHE F 88 TYR 0.009 0.001 TYR B 46 ARG 0.005 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 78) hydrogen bonds : angle 7.55819 ( 234) covalent geometry : bond 0.00378 ( 6320) covalent geometry : angle 0.53025 ( 8530) *********************** 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 129 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7180 (mt-10) REVERT: A 46 TYR cc_start: 0.8101 (m-10) cc_final: 0.7607 (m-10) REVERT: C 42 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8269 (mtt180) REVERT: C 87 ASP cc_start: 0.8079 (m-30) cc_final: 0.7832 (m-30) REVERT: D 42 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.6308 (mmp-170) REVERT: D 46 TYR cc_start: 0.7706 (m-10) cc_final: 0.7388 (m-10) REVERT: D 73 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7378 (mttm) REVERT: E 19 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7491 (mt-10) REVERT: E 34 MET cc_start: 0.8290 (mtt) cc_final: 0.7980 (mtt) REVERT: E 73 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7492 (pttp) REVERT: F 43 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7515 (mt-10) REVERT: F 46 TYR cc_start: 0.8082 (m-10) cc_final: 0.7796 (m-10) REVERT: H 42 ARG cc_start: 0.8523 (mtt180) cc_final: 0.8292 (mtt180) REVERT: H 87 ASP cc_start: 0.8108 (m-30) cc_final: 0.7851 (m-30) REVERT: I 42 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.6292 (mmp-170) REVERT: I 46 TYR cc_start: 0.7665 (m-10) cc_final: 0.7357 (m-10) REVERT: I 73 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7423 (mttm) REVERT: J 19 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7483 (mt-10) REVERT: J 34 MET cc_start: 0.8376 (mtt) cc_final: 0.8082 (mtt) REVERT: J 73 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7507 (pttp) outliers start: 11 outliers final: 6 residues processed: 126 average time/residue: 0.7796 time to fit residues: 114.3970 Evaluate side-chains 114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 22 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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** 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 = 0.4547 r_free = 0.4547 target = 0.187964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.174688 restraints weight = 22342.553| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.14 r_work: 0.4191 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4499 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= 0.234 Angle : 0.592 4.490 8530 Z= 0.346 Chirality : 0.048 0.145 740 Planarity : 0.004 0.026 1150 Dihedral : 5.983 22.628 870 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 2.36 % Allowed : 12.18 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.21), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 70 HIS 0.005 0.001 HIS E 54 PHE 0.015 0.002 PHE A 88 TYR 0.013 0.002 TYR B 46 ARG 0.005 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 78) hydrogen bonds : angle 7.69491 ( 234) covalent geometry : bond 0.00547 ( 6320) covalent geometry : angle 0.59247 ( 8530) *********************** 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 129 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 46 TYR cc_start: 0.8180 (m-10) cc_final: 0.7762 (m-10) REVERT: B 36 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: C 87 ASP cc_start: 0.8023 (m-30) cc_final: 0.7784 (m-30) REVERT: D 42 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.6454 (mmp-170) REVERT: D 46 TYR cc_start: 0.7607 (m-10) cc_final: 0.7257 (m-10) REVERT: D 73 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7438 (mttm) REVERT: E 19 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7636 (mt-10) REVERT: E 34 MET cc_start: 0.8309 (mtt) cc_final: 0.8012 (mtt) REVERT: E 73 LYS cc_start: 0.8452 (mtmt) cc_final: 0.7575 (pttp) REVERT: F 43 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7481 (mt-10) REVERT: F 46 TYR cc_start: 0.8158 (m-10) cc_final: 0.7890 (m-10) REVERT: G 36 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7827 (mtt-85) REVERT: H 87 ASP cc_start: 0.8117 (m-30) cc_final: 0.7855 (m-30) REVERT: I 42 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.6438 (mmp-170) REVERT: I 46 TYR cc_start: 0.7651 (m-10) cc_final: 0.7312 (m-10) REVERT: I 73 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7486 (mttm) REVERT: J 19 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7501 (mt-10) REVERT: J 34 MET cc_start: 0.8376 (mtt) cc_final: 0.8099 (mtt) REVERT: J 73 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7567 (pttp) outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 0.6790 time to fit residues: 98.0426 Evaluate side-chains 117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J residue 43 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.193358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.180021 restraints weight = 22348.316| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 2.18 r_work: 0.4387 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4289 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6320 Z= 0.118 Angle : 0.496 4.271 8530 Z= 0.289 Chirality : 0.045 0.133 740 Planarity : 0.003 0.023 1150 Dihedral : 5.568 19.374 870 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.64 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 35 HIS 0.005 0.001 HIS J 54 PHE 0.008 0.001 PHE A 88 TYR 0.008 0.001 TYR G 52 ARG 0.003 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 78) hydrogen bonds : angle 7.22122 ( 234) covalent geometry : bond 0.00268 ( 6320) covalent geometry : angle 0.49640 ( 8530) *********************** 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 123 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 46 TYR cc_start: 0.7982 (m-10) cc_final: 0.7498 (m-10) REVERT: B 36 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7717 (mtt-85) REVERT: B 41 MET cc_start: 0.8154 (mtt) cc_final: 0.7918 (mtt) REVERT: C 87 ASP cc_start: 0.7995 (m-30) cc_final: 0.7673 (m-30) REVERT: D 42 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.6451 (mmp-170) REVERT: D 46 TYR cc_start: 0.7548 (m-10) cc_final: 0.7256 (m-10) REVERT: D 73 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7533 (mttm) REVERT: E 19 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7506 (mt-10) REVERT: E 34 MET cc_start: 0.8329 (mtt) cc_final: 0.8051 (mtt) REVERT: E 73 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7528 (pttp) REVERT: F 43 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7243 (mt-10) REVERT: F 46 TYR cc_start: 0.8006 (m-10) cc_final: 0.7478 (m-10) REVERT: G 36 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7728 (mtt-85) REVERT: H 87 ASP cc_start: 0.8001 (m-30) cc_final: 0.7679 (m-30) REVERT: I 42 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.6417 (mmp-170) REVERT: I 73 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7465 (mttm) REVERT: J 19 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7495 (mt-10) REVERT: J 34 MET cc_start: 0.8322 (mtt) cc_final: 0.8059 (mtt) REVERT: J 73 LYS cc_start: 0.8407 (mtmt) cc_final: 0.7545 (pttp) outliers start: 9 outliers final: 5 residues processed: 121 average time/residue: 0.6573 time to fit residues: 94.0167 Evaluate side-chains 105 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain D residue 84 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.188229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.174897 restraints weight = 22569.748| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.18 r_work: 0.4335 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4239 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6320 Z= 0.241 Angle : 0.583 4.419 8530 Z= 0.340 Chirality : 0.048 0.142 740 Planarity : 0.004 0.024 1150 Dihedral : 5.875 22.664 870 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 1.82 % Allowed : 13.64 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (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 TRP 0.010 0.002 TRP I 70 HIS 0.005 0.001 HIS E 54 PHE 0.012 0.002 PHE A 88 TYR 0.011 0.002 TYR G 52 ARG 0.004 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 78) hydrogen bonds : angle 7.44794 ( 234) covalent geometry : bond 0.00564 ( 6320) covalent geometry : angle 0.58319 ( 8530) *********************** 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 116 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 46 TYR cc_start: 0.8158 (m-10) cc_final: 0.7792 (m-10) REVERT: B 36 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7874 (mtt-85) REVERT: B 41 MET cc_start: 0.8176 (mtt) cc_final: 0.7967 (mtt) REVERT: C 87 ASP cc_start: 0.8086 (m-30) cc_final: 0.7836 (m-30) REVERT: D 42 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.6534 (mmp-170) REVERT: D 46 TYR cc_start: 0.7569 (m-10) cc_final: 0.7250 (m-10) REVERT: D 73 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7497 (mttm) REVERT: E 19 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7540 (mt-10) REVERT: E 34 MET cc_start: 0.8318 (mtt) cc_final: 0.8047 (mtt) REVERT: E 73 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7566 (pttp) REVERT: F 43 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7462 (mt-10) REVERT: F 46 TYR cc_start: 0.8163 (m-10) cc_final: 0.7887 (m-10) REVERT: G 36 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.7885 (mtt-85) REVERT: H 87 ASP cc_start: 0.8128 (m-30) cc_final: 0.7852 (m-30) REVERT: I 42 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.6534 (mmp-170) REVERT: I 46 TYR cc_start: 0.7715 (m-10) cc_final: 0.7390 (m-10) REVERT: I 73 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7463 (mttm) REVERT: J 19 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7552 (mt-10) REVERT: J 34 MET cc_start: 0.8358 (mtt) cc_final: 0.8098 (mtt) REVERT: J 73 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7568 (pttp) outliers start: 10 outliers final: 8 residues processed: 114 average time/residue: 0.6966 time to fit residues: 93.2843 Evaluate side-chains 110 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.197196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.184289 restraints weight = 22175.950| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.11 r_work: 0.4366 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4267 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6320 Z= 0.123 Angle : 0.497 4.635 8530 Z= 0.289 Chirality : 0.045 0.133 740 Planarity : 0.003 0.024 1150 Dihedral : 5.504 19.335 870 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 2.18 % Allowed : 13.45 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 35 HIS 0.006 0.001 HIS J 54 PHE 0.008 0.001 PHE C 23 TYR 0.012 0.001 TYR B 46 ARG 0.002 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 78) hydrogen bonds : angle 7.12912 ( 234) covalent geometry : bond 0.00285 ( 6320) covalent geometry : angle 0.49747 ( 8530) *********************** 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 120 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7125 (mt-10) REVERT: A 46 TYR cc_start: 0.8003 (m-10) cc_final: 0.7539 (m-10) REVERT: B 36 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7732 (mtt-85) REVERT: B 41 MET cc_start: 0.8146 (mtt) cc_final: 0.7945 (mtt) REVERT: C 87 ASP cc_start: 0.8074 (m-30) cc_final: 0.7759 (m-30) REVERT: D 42 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.6535 (mmp-170) REVERT: D 46 TYR cc_start: 0.7451 (m-10) cc_final: 0.7147 (m-10) REVERT: D 73 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7487 (mttm) REVERT: E 19 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7500 (mt-10) REVERT: E 34 MET cc_start: 0.8333 (mtt) cc_final: 0.8070 (mtt) REVERT: E 36 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.4596 (mmm160) REVERT: E 73 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7540 (pttp) REVERT: G 36 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7728 (mtt-85) REVERT: G 41 MET cc_start: 0.8188 (mtt) cc_final: 0.7861 (mtt) REVERT: H 87 ASP cc_start: 0.8082 (m-30) cc_final: 0.7770 (m-30) REVERT: I 42 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.6518 (mmp-170) REVERT: I 46 TYR cc_start: 0.7489 (m-10) cc_final: 0.7207 (m-10) REVERT: I 73 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7449 (mttm) REVERT: J 19 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7528 (mt-10) REVERT: J 34 MET cc_start: 0.8336 (mtt) cc_final: 0.8079 (mtt) REVERT: J 73 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7569 (pttp) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.6368 time to fit residues: 86.1665 Evaluate side-chains 108 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 9 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 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 J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.194671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.181814 restraints weight = 22227.410| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 2.14 r_work: 0.4389 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4292 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4772 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= 0.173 Angle : 0.530 4.394 8530 Z= 0.308 Chirality : 0.047 0.138 740 Planarity : 0.003 0.023 1150 Dihedral : 5.568 20.781 870 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 2.00 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 70 HIS 0.006 0.001 HIS J 54 PHE 0.009 0.002 PHE H 23 TYR 0.019 0.002 TYR F 46 ARG 0.003 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 78) hydrogen bonds : angle 7.14682 ( 234) covalent geometry : bond 0.00405 ( 6320) covalent geometry : angle 0.52992 ( 8530) *********************** 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 108 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7785 (mtt-85) REVERT: C 87 ASP cc_start: 0.8017 (m-30) cc_final: 0.7745 (m-30) REVERT: D 42 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.6571 (mmp-170) REVERT: D 73 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7471 (mttm) REVERT: E 19 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7535 (mt-10) REVERT: E 34 MET cc_start: 0.8299 (mtt) cc_final: 0.8030 (mtt) REVERT: E 73 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7559 (pttp) REVERT: F 43 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7128 (mt-10) REVERT: G 36 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7755 (mtt-85) REVERT: G 41 MET cc_start: 0.8303 (mtt) cc_final: 0.8002 (mtt) REVERT: H 87 ASP cc_start: 0.8040 (m-30) cc_final: 0.7744 (m-30) REVERT: I 42 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.6544 (mmp-170) REVERT: I 46 TYR cc_start: 0.7529 (m-10) cc_final: 0.7189 (m-10) REVERT: I 73 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7464 (mttm) REVERT: J 19 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7563 (mt-10) REVERT: J 34 MET cc_start: 0.8313 (mtt) cc_final: 0.8044 (mtt) REVERT: J 73 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7565 (pttp) outliers start: 11 outliers final: 7 residues processed: 106 average time/residue: 0.7252 time to fit residues: 90.0336 Evaluate side-chains 101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4566 r_free = 0.4566 target = 0.189285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.175899 restraints weight = 22349.164| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.19 r_work: 0.4369 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4272 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6320 Z= 0.221 Angle : 0.575 4.465 8530 Z= 0.333 Chirality : 0.048 0.143 740 Planarity : 0.004 0.025 1150 Dihedral : 5.745 22.144 870 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 1.45 % Allowed : 14.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP E 70 HIS 0.006 0.001 HIS E 54 PHE 0.013 0.002 PHE H 23 TYR 0.025 0.002 TYR F 46 ARG 0.004 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 78) hydrogen bonds : angle 7.27235 ( 234) covalent geometry : bond 0.00518 ( 6320) covalent geometry : angle 0.57453 ( 8530) ********************** 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: 8 poor density : 99 time to evaluate : 1.329 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: 0.7753 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 87 ASP cc_start: 0.8083 (m-30) cc_final: 0.7793 (m-30) REVERT: D 42 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.6616 (mmp-170) REVERT: D 73 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7513 (mttm) REVERT: E 19 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7568 (mt-10) REVERT: E 34 MET cc_start: 0.8329 (mtt) cc_final: 0.8038 (mtt) REVERT: E 73 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7569 (pttp) REVERT: F 43 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7193 (mt-10) REVERT: G 41 MET cc_start: 0.8306 (mtt) cc_final: 0.7962 (mtt) REVERT: H 87 ASP cc_start: 0.8089 (m-30) cc_final: 0.7798 (m-30) REVERT: I 42 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.6601 (mmp-170) REVERT: I 46 TYR cc_start: 0.7541 (m-10) cc_final: 0.7185 (m-10) REVERT: I 73 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7492 (mttm) REVERT: J 19 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7665 (mt-10) REVERT: J 34 MET cc_start: 0.8311 (mtt) cc_final: 0.8044 (mtt) REVERT: J 73 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7585 (pttp) outliers start: 8 outliers final: 6 residues processed: 105 average time/residue: 0.7905 time to fit residues: 97.9735 Evaluate side-chains 104 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG 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 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 30 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 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 J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.193842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.180827 restraints weight = 22330.052| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 2.18 r_work: 0.4386 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4284 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4890 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= 0.172 Angle : 0.532 4.445 8530 Z= 0.309 Chirality : 0.047 0.140 740 Planarity : 0.003 0.024 1150 Dihedral : 5.630 20.932 870 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 1.82 % Allowed : 14.36 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 70 HIS 0.007 0.001 HIS J 54 PHE 0.010 0.002 PHE H 23 TYR 0.025 0.002 TYR F 46 ARG 0.003 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 78) hydrogen bonds : angle 7.17589 ( 234) covalent geometry : bond 0.00404 ( 6320) covalent geometry : angle 0.53227 ( 8530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6369.47 seconds wall clock time: 111 minutes 0.77 seconds (6660.77 seconds total)