Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:49:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/12_2022/7zh7_14726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/12_2022/7zh7_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_14726/12_2022/7zh7_14726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/12_2022/7zh7_14726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/12_2022/7zh7_14726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh7_14726/12_2022/7zh7_14726.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 5.50, per 1000 atoms: 0.48 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: 8.23 Conformation dependent library (CDL) restraints added in 924.9 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 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: 3.92 Time building geometry restraints manager: 8.71 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 - 11.81: 4331 11.81 - 23.62: 336 23.62 - 35.43: 93 35.43 - 47.24: 40 47.24 - 59.06: 30 Dihedral angle restraints: 4830 sinusoidal: 1970 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 4827 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 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. 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: 0.550 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: 0.150 Extract box with map and model: 4.130 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 37.440 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 % 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 *********************** 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 : 0.884 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.5960 time to fit residues: 133.8652 Evaluate side-chains 144 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1479 ------------------------------------------------------------------------------- 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: 7.9990 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: 6.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 D 91 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 6320 Z= 0.428 Angle : 0.718 6.679 8530 Z= 0.415 Chirality : 0.052 0.151 740 Planarity : 0.005 0.038 1150 Dihedral : 6.312 22.468 870 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 2.18 % 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: -4.48 (0.18), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.14), residues: 740 *********************** 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 158 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.879 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 outliers start: 12 outliers final: 3 residues processed: 156 average time/residue: 0.6242 time to fit residues: 114.4903 Evaluate side-chains 124 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3578 time to fit residues: 2.4933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 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 E 54 HIS F 54 HIS J 54 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4266 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= 0.323 Angle : 0.600 4.923 8530 Z= 0.348 Chirality : 0.047 0.138 740 Planarity : 0.003 0.025 1150 Dihedral : 6.024 20.597 870 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.55 % 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: -4.53 (0.18), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.14), residues: 740 *********************** 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 128 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 128 average time/residue: 0.5718 time to fit residues: 87.7393 Evaluate side-chains 117 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7601 time to fit residues: 1.7593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 HIS ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4718 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= 0.326 Angle : 0.579 4.220 8530 Z= 0.340 Chirality : 0.047 0.141 740 Planarity : 0.003 0.022 1150 Dihedral : 5.914 22.766 870 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer Outliers : 0.36 % 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: -4.56 (0.19), residues: 740 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.15), residues: 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.861 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 outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.5227 time to fit residues: 77.3108 Evaluate side-chains 111 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1308 time to fit residues: 1.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0796 > 50: distance: 112 - 303: 36.468 distance: 228 - 233: 33.877 distance: 233 - 234: 40.923 distance: 233 - 241: 46.175 distance: 234 - 235: 37.218 distance: 234 - 237: 20.937 distance: 235 - 236: 39.848 distance: 235 - 247: 40.017 distance: 237 - 238: 16.772 distance: 237 - 243: 46.422 distance: 237 - 244: 18.190 distance: 238 - 240: 23.047 distance: 240 - 245: 29.685 distance: 240 - 246: 43.562 distance: 247 - 248: 38.369 distance: 248 - 249: 9.924 distance: 248 - 251: 36.962 distance: 248 - 260: 53.990 distance: 249 - 250: 28.331 distance: 249 - 268: 13.913 distance: 251 - 252: 36.775 distance: 251 - 262: 37.920 distance: 253 - 255: 26.495 distance: 254 - 256: 8.628 distance: 255 - 257: 12.112 distance: 255 - 265: 14.095 distance: 256 - 257: 32.377 distance: 256 - 266: 33.626 distance: 258 - 267: 56.516 distance: 268 - 269: 49.459 distance: 268 - 276: 39.481 distance: 269 - 270: 10.821 distance: 269 - 272: 11.199 distance: 269 - 277: 48.964 distance: 270 - 271: 4.444 distance: 272 - 279: 29.669 distance: 273 - 275: 40.677 distance: 280 - 281: 39.893 distance: 281 - 284: 42.226 distance: 282 - 283: 40.204 distance: 284 - 287: 25.475 distance: 284 - 288: 25.198 distance: 284 - 289: 47.514 distance: 290 - 295: 39.817 distance: 291 - 292: 39.494 distance: 291 - 294: 28.702 distance: 294 - 297: 11.324 distance: 294 - 298: 45.079 distance: 294 - 299: 28.081 distance: 300 - 301: 38.647 distance: 300 - 309: 39.185 distance: 301 - 302: 63.994 distance: 301 - 304: 39.902 distance: 301 - 310: 57.068 distance: 302 - 303: 31.512 distance: 302 - 317: 63.743 distance: 304 - 305: 8.950 distance: 304 - 311: 40.956 distance: 304 - 312: 40.142 distance: 305 - 306: 41.119 distance: 305 - 313: 50.991 distance: 305 - 314: 32.367 distance: 306 - 308: 40.988 distance: 308 - 315: 39.892 distance: 308 - 316: 39.189 distance: 317 - 318: 19.785 distance: 317 - 328: 15.694 distance: 317 - 475: 35.896 distance: 318 - 319: 30.596 distance: 318 - 321: 46.034 distance: 318 - 329: 36.849 distance: 319 - 320: 48.389 distance: 321 - 322: 31.804 distance: 321 - 330: 3.179 distance: 321 - 331: 42.756 distance: 322 - 323: 16.302 distance: 322 - 332: 37.645 distance: 322 - 333: 4.499 distance: 323 - 324: 21.331 distance: 323 - 334: 19.477 distance: 323 - 335: 4.020 distance: 324 - 325: 66.757 distance: 324 - 336: 24.060 distance: 325 - 326: 53.118 distance: 325 - 327: 58.088 distance: 326 - 337: 14.080 distance: 326 - 338: 42.163 distance: 327 - 340: 56.512 distance: 341 - 342: 40.917 distance: 342 - 343: 39.354 distance: 343 - 344: 57.376 distance: 343 - 348: 23.340 distance: 348 - 349: 23.176 distance: 348 - 354: 22.271 distance: 349 - 352: 40.416 distance: 350 - 362: 69.534 distance: 352 - 356: 39.553 distance: 352 - 357: 40.536 distance: 353 - 354: 39.296 distance: 354 - 361: 40.316 distance: 362 - 363: 70.263 distance: 362 - 366: 39.543 distance: 363 - 364: 68.240 distance: 363 - 367: 40.627 distance: 364 - 365: 57.415 distance: 364 - 369: 35.011