Starting phenix.real_space_refine on Fri Mar 15 11:28:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/03_2024/7zh7_14726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/03_2024/7zh7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/03_2024/7zh7_14726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/03_2024/7zh7_14726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/03_2024/7zh7_14726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/03_2024/7zh7_14726.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.69, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 8.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.17 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: 3.78 Time building geometry restraints manager: 9.10 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: 99.90 - 106.72: 166 106.72 - 113.55: 11722 113.55 - 120.37: 4523 120.37 - 127.20: 4086 127.20 - 134.02: 113 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 1.850 nonbonded pdb="HH21 ARG A 90 " pdb=" OE2 GLU D 19 " model vdw 1.762 1.850 nonbonded pdb="HH11 ARG F 64 " pdb=" OH TYR G 59 " model vdw 1.855 1.850 nonbonded pdb="HH11 ARG G 64 " pdb=" OH TYR I 59 " model vdw 1.857 1.850 nonbonded pdb="HH11 ARG A 64 " pdb=" OH TYR B 59 " model vdw 1.857 1.850 ... (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 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 3.890 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 40.070 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.730 ------------------------------------------------------------------------------- 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= 0.182 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.910 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: 0.6901 time to fit residues: 152.5736 Evaluate side-chains 146 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 B 54 HIS D 54 HIS E 54 HIS F 54 HIS F 91 HIS G 54 HIS H 54 HIS I 54 HIS J 54 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 6320 Z= 0.439 Angle : 0.708 5.845 8530 Z= 0.409 Chirality : 0.051 0.156 740 Planarity : 0.005 0.045 1150 Dihedral : 6.190 21.342 870 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.18 % Allowed : 7.82 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.13), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 20 HIS 0.006 0.002 HIS E 54 PHE 0.016 0.002 PHE E 23 TYR 0.012 0.002 TYR I 21 ARG 0.005 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.954 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: 0.7610 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 56 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6682 (ttp-170) REVERT: A 87 ASP cc_start: 0.7831 (m-30) cc_final: 0.7607 (m-30) REVERT: B 19 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7013 (mm-30) REVERT: C 52 TYR cc_start: 0.8408 (m-80) cc_final: 0.8136 (m-80) REVERT: D 42 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.6336 (mmp-170) REVERT: D 46 TYR cc_start: 0.7675 (m-10) cc_final: 0.7466 (m-80) REVERT: D 73 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7188 (mttm) REVERT: E 34 MET cc_start: 0.8166 (mtt) cc_final: 0.7934 (mtt) REVERT: E 73 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7219 (pttp) REVERT: F 43 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7394 (mt-10) REVERT: F 56 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6684 (ttp-170) REVERT: G 19 GLU cc_start: 0.7211 (mm-30) cc_final: 0.7009 (mm-30) REVERT: G 42 ARG cc_start: 0.8308 (mtt180) cc_final: 0.8105 (mtt180) REVERT: H 52 TYR cc_start: 0.8398 (m-80) cc_final: 0.8135 (m-80) REVERT: I 42 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.6317 (mmp-170) REVERT: I 46 TYR cc_start: 0.7673 (m-10) cc_final: 0.7471 (m-80) REVERT: I 73 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7163 (mttm) REVERT: J 34 MET cc_start: 0.8161 (mtt) cc_final: 0.7910 (mtt) REVERT: J 73 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7225 (pttp) outliers start: 12 outliers final: 4 residues processed: 160 average time/residue: 0.7196 time to fit residues: 133.5126 Evaluate side-chains 129 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 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 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 35 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 54 HIS ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS F 54 HIS G 54 HIS J 54 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3873 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= 0.320 Angle : 0.604 5.518 8530 Z= 0.349 Chirality : 0.048 0.140 740 Planarity : 0.004 0.027 1150 Dihedral : 5.967 19.605 870 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.27 % Allowed : 10.55 % Favored : 88.18 % 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 (0.19), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (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 0.008 0.002 PHE J 23 TYR 0.009 0.001 TYR B 46 ARG 0.004 0.001 ARG D 36 *********************** 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 137 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7033 (mt-10) REVERT: B 19 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7119 (mm-30) REVERT: C 42 ARG cc_start: 0.8442 (mtt180) cc_final: 0.8140 (mtt180) REVERT: D 42 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.6230 (mmp80) REVERT: D 46 TYR cc_start: 0.7653 (m-10) cc_final: 0.7427 (m-80) REVERT: D 73 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7200 (mttm) REVERT: E 34 MET cc_start: 0.8197 (mtt) cc_final: 0.7880 (mtt) REVERT: E 73 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7246 (pttp) REVERT: F 43 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7293 (mt-10) REVERT: G 19 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7071 (mm-30) REVERT: H 42 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8140 (mtt180) REVERT: I 42 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.6171 (mmp80) REVERT: I 46 TYR cc_start: 0.7666 (m-10) cc_final: 0.7433 (m-80) REVERT: I 73 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7115 (mttm) REVERT: J 34 MET cc_start: 0.8177 (mtt) cc_final: 0.7871 (mtt) REVERT: J 73 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7290 (pttp) outliers start: 7 outliers final: 4 residues processed: 137 average time/residue: 0.6521 time to fit residues: 104.7938 Evaluate side-chains 123 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 47 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6320 Z= 0.285 Angle : 0.546 4.175 8530 Z= 0.322 Chirality : 0.046 0.135 740 Planarity : 0.003 0.025 1150 Dihedral : 5.788 20.658 870 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.09 % Allowed : 11.64 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.49 (0.20), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.15), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 70 HIS 0.006 0.001 HIS J 54 PHE 0.010 0.002 PHE E 23 TYR 0.011 0.001 TYR B 46 ARG 0.004 0.001 ARG B 36 *********************** 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 125 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7052 (mt-10) REVERT: B 36 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7413 (mtt-85) REVERT: D 42 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.6283 (mmp-170) REVERT: D 46 TYR cc_start: 0.7566 (m-10) cc_final: 0.7257 (m-10) REVERT: D 73 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7205 (mttm) REVERT: E 34 MET cc_start: 0.8178 (mtt) cc_final: 0.7863 (mtt) REVERT: E 73 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7298 (pttp) REVERT: F 43 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7287 (mt-10) REVERT: I 42 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.6286 (mmp-170) REVERT: I 46 TYR cc_start: 0.7583 (m-10) cc_final: 0.7241 (m-10) REVERT: I 73 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7212 (mttm) REVERT: J 34 MET cc_start: 0.8177 (mtt) cc_final: 0.7869 (mtt) REVERT: J 73 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7305 (pttp) outliers start: 6 outliers final: 4 residues processed: 124 average time/residue: 0.6330 time to fit residues: 92.4861 Evaluate side-chains 113 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4325 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= 0.195 Angle : 0.495 4.274 8530 Z= 0.291 Chirality : 0.045 0.134 740 Planarity : 0.003 0.025 1150 Dihedral : 5.517 19.144 870 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.45 % Allowed : 12.73 % Favored : 85.82 % 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: -4.38 (0.21), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 70 HIS 0.005 0.001 HIS J 54 PHE 0.008 0.001 PHE F 88 TYR 0.009 0.001 TYR B 46 ARG 0.002 0.000 ARG B 36 *********************** 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 128 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 36 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7411 (mtt-85) REVERT: C 42 ARG cc_start: 0.8416 (mtt180) cc_final: 0.8109 (mtt180) REVERT: D 42 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.6299 (mmp-170) REVERT: D 46 TYR cc_start: 0.7515 (m-10) cc_final: 0.7216 (m-10) REVERT: D 73 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7231 (mttm) REVERT: E 34 MET cc_start: 0.8177 (mtt) cc_final: 0.7868 (mtt) REVERT: E 73 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7326 (pttp) REVERT: F 43 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7116 (mt-10) REVERT: H 42 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8114 (mtt180) REVERT: I 42 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.6305 (mmp-170) REVERT: I 46 TYR cc_start: 0.7517 (m-10) cc_final: 0.7173 (m-10) REVERT: I 73 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7251 (mttm) REVERT: J 34 MET cc_start: 0.8191 (mtt) cc_final: 0.7906 (mtt) REVERT: J 73 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7328 (pttp) outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 0.6156 time to fit residues: 90.8942 Evaluate side-chains 118 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4642 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= 0.379 Angle : 0.597 4.534 8530 Z= 0.349 Chirality : 0.048 0.142 740 Planarity : 0.004 0.025 1150 Dihedral : 5.853 23.081 870 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 1.09 % Allowed : 13.82 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.55 (0.21), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 70 HIS 0.005 0.001 HIS J 54 PHE 0.012 0.002 PHE F 88 TYR 0.010 0.002 TYR B 46 ARG 0.004 0.001 ARG F 90 *********************** 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 115 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7067 (mt-10) REVERT: A 87 ASP cc_start: 0.7842 (m-30) cc_final: 0.7562 (m-30) REVERT: B 36 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7515 (mtt-85) REVERT: B 41 MET cc_start: 0.8190 (mtt) cc_final: 0.7955 (mtt) REVERT: D 19 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6642 (mm-30) REVERT: D 42 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.6394 (mmp-170) REVERT: D 46 TYR cc_start: 0.7674 (m-10) cc_final: 0.7321 (m-10) REVERT: D 73 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7160 (mttm) REVERT: E 34 MET cc_start: 0.8159 (mtt) cc_final: 0.7848 (mtt) REVERT: E 73 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7252 (pttp) REVERT: I 19 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6778 (mm-30) REVERT: I 42 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.6396 (mmp-170) REVERT: I 46 TYR cc_start: 0.7721 (m-10) cc_final: 0.7346 (m-10) REVERT: I 73 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7169 (mttm) REVERT: J 34 MET cc_start: 0.8155 (mtt) cc_final: 0.7847 (mtt) REVERT: J 73 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7292 (pttp) outliers start: 6 outliers final: 5 residues processed: 115 average time/residue: 0.5656 time to fit residues: 77.6866 Evaluate side-chains 102 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 24 LEU 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 38 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4787 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= 0.331 Angle : 0.574 4.401 8530 Z= 0.335 Chirality : 0.047 0.143 740 Planarity : 0.003 0.026 1150 Dihedral : 5.802 21.732 870 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 0.91 % Allowed : 15.09 % 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: -4.52 (0.21), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 70 HIS 0.005 0.001 HIS J 54 PHE 0.010 0.002 PHE C 23 TYR 0.011 0.002 TYR B 46 ARG 0.003 0.001 ARG F 90 *********************** 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 105 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.871 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: 0.7452 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 87 ASP cc_start: 0.7868 (m-30) cc_final: 0.7520 (m-30) REVERT: B 41 MET cc_start: 0.8126 (mtt) cc_final: 0.7893 (mtt) REVERT: D 19 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6836 (mm-30) REVERT: D 42 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.6487 (mmp-170) REVERT: D 46 TYR cc_start: 0.7448 (m-10) cc_final: 0.7142 (m-10) REVERT: D 73 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7216 (mttm) REVERT: E 34 MET cc_start: 0.8186 (mtt) cc_final: 0.7866 (mtt) REVERT: E 73 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7281 (pttp) REVERT: F 87 ASP cc_start: 0.7827 (m-30) cc_final: 0.7553 (m-30) REVERT: G 41 MET cc_start: 0.8195 (mtt) cc_final: 0.7869 (mtt) REVERT: I 19 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6864 (mm-30) REVERT: I 42 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.6457 (mmp-170) REVERT: I 46 TYR cc_start: 0.7472 (m-10) cc_final: 0.7126 (m-10) REVERT: I 73 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7199 (mttm) REVERT: J 34 MET cc_start: 0.8181 (mtt) cc_final: 0.7867 (mtt) REVERT: J 73 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7283 (pttp) outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 0.6025 time to fit residues: 75.6766 Evaluate side-chains 101 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4801 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= 0.257 Angle : 0.529 4.214 8530 Z= 0.309 Chirality : 0.046 0.136 740 Planarity : 0.003 0.024 1150 Dihedral : 5.633 21.619 870 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 0.91 % Allowed : 15.45 % 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: -4.47 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 70 HIS 0.006 0.001 HIS J 54 PHE 0.010 0.002 PHE H 23 TYR 0.014 0.001 TYR B 52 ARG 0.003 0.000 ARG F 90 *********************** 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 110 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.935 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: A 43 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 87 ASP cc_start: 0.7819 (m-30) cc_final: 0.7507 (m-30) REVERT: B 41 MET cc_start: 0.8134 (mtt) cc_final: 0.7885 (mtt) REVERT: D 19 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 42 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.6491 (mmp-170) REVERT: D 46 TYR cc_start: 0.7239 (m-10) cc_final: 0.6923 (m-10) REVERT: D 73 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7259 (mttm) REVERT: E 34 MET cc_start: 0.8175 (mtt) cc_final: 0.7861 (mtt) REVERT: E 73 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7266 (pttp) REVERT: F 87 ASP cc_start: 0.7832 (m-30) cc_final: 0.7590 (m-30) REVERT: G 41 MET cc_start: 0.8204 (mtt) cc_final: 0.7907 (mtt) REVERT: I 19 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6799 (mm-30) REVERT: I 42 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.6441 (mmp-170) REVERT: I 46 TYR cc_start: 0.7281 (m-10) cc_final: 0.6960 (m-10) REVERT: I 73 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7176 (mttm) REVERT: J 34 MET cc_start: 0.8158 (mtt) cc_final: 0.7880 (mtt) REVERT: J 73 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7290 (pttp) outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 0.5811 time to fit residues: 76.4514 Evaluate side-chains 101 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4906 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= 0.334 Angle : 0.569 4.391 8530 Z= 0.333 Chirality : 0.048 0.142 740 Planarity : 0.003 0.025 1150 Dihedral : 5.773 22.517 870 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.91 % Allowed : 15.64 % Favored : 83.45 % 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 : -3.43 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 70 HIS 0.006 0.001 HIS J 54 PHE 0.012 0.002 PHE H 23 TYR 0.016 0.002 TYR B 52 ARG 0.003 0.001 ARG F 90 *********************** 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 104 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.913 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: 0.7412 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 87 ASP cc_start: 0.7848 (m-30) cc_final: 0.7537 (m-30) REVERT: B 41 MET cc_start: 0.8213 (mtt) cc_final: 0.7956 (mtt) REVERT: D 19 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6840 (mm-30) REVERT: D 42 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.6491 (mmp-170) REVERT: D 46 TYR cc_start: 0.7272 (m-10) cc_final: 0.6955 (m-10) REVERT: D 73 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7244 (mttm) REVERT: E 34 MET cc_start: 0.8183 (mtt) cc_final: 0.7875 (mtt) REVERT: E 73 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7236 (pttp) REVERT: F 87 ASP cc_start: 0.7861 (m-30) cc_final: 0.7624 (m-30) REVERT: I 19 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6885 (mm-30) REVERT: I 42 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.6528 (mmp-170) REVERT: I 46 TYR cc_start: 0.7302 (m-10) cc_final: 0.6972 (m-10) REVERT: I 73 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7182 (mttm) REVERT: J 34 MET cc_start: 0.8176 (mtt) cc_final: 0.7886 (mtt) REVERT: J 73 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7277 (pttp) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.5887 time to fit residues: 73.0270 Evaluate side-chains 99 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.2980 chunk 64 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6320 Z= 0.132 Angle : 0.465 4.497 8530 Z= 0.271 Chirality : 0.044 0.135 740 Planarity : 0.003 0.022 1150 Dihedral : 5.306 17.866 870 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.91 % Allowed : 15.09 % 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: -4.29 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.008 0.001 HIS J 54 PHE 0.010 0.002 PHE C 89 TYR 0.013 0.001 TYR B 52 ARG 0.002 0.000 ARG H 36 ********************** 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 118 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 46 TYR cc_start: 0.7538 (m-10) cc_final: 0.7207 (m-10) REVERT: B 41 MET cc_start: 0.8035 (mtt) cc_final: 0.7832 (mtt) REVERT: D 42 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.6284 (mmp-170) REVERT: D 73 LYS cc_start: 0.8180 (mtmt) cc_final: 0.6368 (mmmt) REVERT: E 34 MET cc_start: 0.8186 (mtt) cc_final: 0.7933 (mtt) REVERT: E 73 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7260 (pttp) REVERT: F 87 ASP cc_start: 0.7778 (m-30) cc_final: 0.7534 (m-30) REVERT: I 19 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6666 (mm-30) REVERT: I 42 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.6250 (mmp-170) REVERT: I 73 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7237 (mttm) REVERT: J 34 MET cc_start: 0.8164 (mtt) cc_final: 0.7900 (mtt) REVERT: J 73 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7289 (pttp) outliers start: 5 outliers final: 2 residues processed: 116 average time/residue: 0.5252 time to fit residues: 74.1025 Evaluate side-chains 102 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.186606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.173372 restraints weight = 22310.818| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.12 r_work: 0.4156 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4977 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= 0.380 Angle : 0.593 4.490 8530 Z= 0.346 Chirality : 0.049 0.143 740 Planarity : 0.004 0.024 1150 Dihedral : 5.724 22.571 870 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 0.73 % Allowed : 15.27 % 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: -4.46 (0.22), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.17), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 70 HIS 0.006 0.001 HIS J 54 PHE 0.012 0.002 PHE H 23 TYR 0.017 0.002 TYR F 46 ARG 0.004 0.001 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.53 seconds wall clock time: 61 minutes 23.32 seconds (3683.32 seconds total)